No, they can't be enchanted, because they aren't masterwork and can never be, and all magic weapons must be crafted with a masterwork base.

Creating Magic Weapons

To create a magic weapon, a character needs a heat source and some iron, wood, or leatherworking tools. She also needs a supply of materials, the most obvious being the weapon or the pieces of the weapon to be assembled. Only a masterwork weapon can become a magic weapon, and the masterwork cost is added to the total cost to determine final market value.

It is quite plain that they are not masterwork by default, given the lack of +1 to attack rolls. So let's suppose we want to upgrade them. But it is impossible for an existing unarmed strike to be made masterwork, per this clause in Weapons:

You can’t add the masterwork quality to a weapon after it is created; it must be crafted as a masterwork weapon (see the Craft skill).

All right, let's try making a new one that's masterwork. This fails because unarmed strikes are not manufactured weapons, and you can't manufacture a weapon with the Craft skill if it's specifically not manufactured at all.

Glossary — manufactured weapons:

This category also includes […] in essence, any weapon that is not intrinsic to the creature.

Monk's class features do not help with this, since Craft is not an effect and neither enhances nor improves anything:

A monk’s unarmed strike is treated both as a manufactured weapon and a natural weapon for the purpose of spells and effects that enhance or improve either manufactured weapons or natural weapons.

How about buying one? You might actually be able to buy an ordinary unarmed strike, since they're listed in the Equipment section in the Weapons table, and you needn't pay anything for it*. Unfortunately, per the quote on MW weapons, a weapon must be crafted as masterwork to be MW, and per the preceding this is not possible even for NPCs. There might be an exception, as there seems to be for magic oils, which you can buy in shops but not craft, except that nowhere is "MW unarmed strike" listed for sale.

Magic fang and company do not make a weapon into a "magic weapon"; rather, they give a weapon a +1 enhancement bonus (and the ability to bypass DR /magic because of that), which is not technically the same thing. And while all magic weapons are masterwork by definition as well as by prerequisite, magic fang and friends do not have to be interpreted as giving a weapon retroactive masterwork status, for essentially the same reason, which is fortunate as otherwise the rules would create some bizarre and abusive situations†.

Magic Fang

Magic fang gives one natural weapon of the subject a +1 enhancement bonus on attack and damage rolls.

Magic Weapon

Magic weapon gives a weapon a +1 enhancement bonus on attack and damage rolls. (An enhancement bonus does not stack with a masterwork weapon’s +1 bonus on attack rolls.) You can’t cast this spell on a natural weapon, such as an unarmed strike (instead, see magic fang). A monk’s unarmed strike is considered a weapon, and thus it can be enhanced by this spell.

Magic Weapons

All magic weapons are also masterwork weapons, but their masterwork bonus on attack rolls does not stack with their enhancement bonus on attack rolls.

Special Abilities

Some monsters are vulnerable to magic weapons. Any weapon with at least a +1 magical enhancement bonus on attack and damage rolls overcomes the damage reduction of these monsters.

Note the phrasing of the last quote; they are described as vulnerable to magic weapons, but that's not the rules text, just the plain description, since vulnerability is not defined (except in the incompatible context of energy vulnerability; it should be clear that DR 5/magic does not mean that a +1 longsword does 50% extra damage as well as overcoming DR). The actual rules say that any weapon with a +1 magical enhancement bonus (whether or not the weapon is, per se, a "magic weapon" itself otherwise) overcomes that DR.

(emphasis added to quotes)

* This is, to my mind, patently absurd, but hey, RAW. Monks won't be proficient with those unarmed strikes, but hey, RAW.
† For example, casting magic weapon to increase the price of a club from 0gp to 300gp (permanently? who knows!) and selling it. Or casting magic weapon on any plain weapon to make it masterwork for future crafting. There is a Pathfinder spell for this purpose. It does nothing else‡, is a level higher, costs as much as crafting a MW weapon in the first place, and takes an hour to cast. Allowing magic weapon to do this for free in a standard action is ridiculous.
‡ It has this excellent provision: "If the target object has no masterwork equivalent, the spell has no effect." Doesn't work on unarmed strikes, as they appear to have no MW equivalent and are not objects.

This seems balanced

You have done an excellent job of identifying the potential issues with your homebrew. I can see no reason why you can't use it for playtesting. It is certainly a power-positive change over the standard Way of the Kensai monk. However that tradition is typically underpowered to begin with so this bring it back into line with the other traditions.

Are there any loopholes, ambiguities or other issues in the wording of the class feature?

Feature is fairly well worded, I can only spot one potential issue. It is something you have already partly identified and would probably make a sensible ruling on the first time you encounter it. How does the damage die relate to magical weapons?

This special attack must use your Martial Arts die for damage, even if the weapon could normally use a larger damage die.

As you already identified this feature synthesizes well with magic weapons that deal additional damage. Is the intent for this to replace only the primary damage dice or all of them? For instance; if I had a Frosthammer that dealt 1d10 Bludgeoning + 1d6 Cold damage and had a Martial Arts die of 1d8 what would be my damage roll with this ability? 1d8(B) + 1d6 (Cold) or 1d8(B) + 1d8 (Cold)?

Is the modified subclass still reasonably balanced relative to other Monks in terms of combat effectiveness?

If anything this change makes this tradition more balanced than it was. Way of the Kensai is weaker than the other non-spellcasting traditions anyway. This change is likely something that should have been there all along. Potentially your concerns about magic weapons will lead to it being overpowered but that will entirely depend on the available of magic items within your campaign.

Would giving up any of the standard Kensei (or Monk) class features bring the balance back into line?

I don't think this is necessary as it is mostly already balanced. But if you do find in playtesting that it is stronger than expected any of the suggestions you make could be a good fix.