Part of the benefit of the arcane discovery alchemical affinity says, "Additionally, you may copy spells from an alchemist's formula book into your spellbook just as you could with another wizard's spellbook." So Magical Marketplace's author, at least, believed it normally impossible for a wizard to copy into his spellbook a formula from an alchemist's formula book.
(Further, the alchemist's supernatural ability alchemy says, "A wizard, however, cannot learn spells from a formula book," and while Pathfinder isn't as clear as it should be when tossing around a very pregnant word like learn, Adding Spells to a Wizard's Spellbook nonetheless says, "If the [Spellcraft skill] check fails, the wizard cannot understand or copy the spell" (emphasis mine). The text continues immediately after, saying, "He cannot attempt to learn or copy that spell again until one week has passed" (emphasis mine). Parallelism makes understand and learn synonyms here, so a wizard, even after waiting a week, still won't be able to make that Spellcraft check to copy a formula because a wizard can't learn spells from a formula book in the first place. Note that I don't like this ruling as much as I like the anecdotal evidence from Marketplace because whenever the GM must make a ruling based on a rule's syntax there's usually more than one possible reading, making disagreements and hard feelings a possibility, so make of this what you will.)
A house rule could allow copying formulas into spellbooks anyway, despite the existence of alchemical affinity
A GM that makes a house rule that allows the PC to add his handful of appropriate alchemist's formulas to his wizard's spellbook (and still requires time and money to transcribe them) needn't worry that the PC is attempting some kind of crazy power-grab. Under such a house rule, a wizard who, late in his career, decides to take levels in alchemist trades versatility for power… and makes a completely uneven trade.
A Wizard with hundreds of spells in their spell book cannot cast more than any other Wizard of the same level. Two Wizards of equal level prepare the same number of spells and can cast the same number of spell slots.
The Wizard with the large repertoire has more options and can fine-tune their selections if they know what they are going to face. Most adventurers don't have that much insight into what they are going to face so the advantage may be marginal.
On the other hand, a large repertoire can be a boon if they have the time, resources, and inclination to prepare scrolls ahead of adventures.
Best Answer
As you say, a Wizard can learn spells from spellbook they find. So the question here is whether wizardly enemies will have spellbooks on them when they are defeated.
That's entirely up to the DM. Like any piece of loot, any enemy could be carrying a spellbook for whatever reason. If the DM wants the players to find the defeated Mage's spellbook, they will. There are a multitude of reasons for why a Mage would or wouldn't be carrying their spellbook on their person - it's the DM's choice to give the players access to this (fairly valuable) piece of treasure or not.
Remember that a Wizard doesn't require their spellbook to cast their spells (unless they want to cast them as rituals), so it's perfectly reasonable for a Mage to have hidden their spellbook somewhere once they prepared their day's spells.
So if you're asking this as a DM, the answer is that it's up to you. If you're asking as a player, the answer is that it's up to the DM, but it might well be worth your while to search the lairs/houses/dens/homes/castles/towers/whatever of enemy Mages you defeat.