It does take two spell slots.
The first line of the spell describes what happens when you cast the Glyph of Warding:
When you cast this spell, you inscribe a glyph that harms other creatures...
Later, it specifies that if you choose the spell glyph option, you cast the spell you choose to store (emphasis added):
You can store a prepared spell of 3rd level or lower in the glyph by casting it as part of creating the glyph.
PHB 201 specifies that when the "casting" wording is used, it uses up a spell slot:
When a character casts a spell, he or she expends a slot of that spell’s level or higher, effectively “filling” a slot with the spell.
This interpretation is consistent with other game mechanics that are more explicit about how this works. For example, contingency works this way:
You cast that spell, called the contingent spell, as part of casting contingency, expending Spell Slots for both, but the contingent spell doesn't come into effect.
or the ring of spell storing:
Any creature can Cast a Spell of 1st through 5th level into the ring by touching the ring as the spell is cast. The spell has no effect, other than to be stored in the ring.
Yes you can cast spells that target self into the glyph
Spells that target "self" meet all the criteria for allowed spells
Glyph of Warding describes all the limitations for which spells can be stored in it:
You can store a prepared spell of 3rd level or lower in the glyph by
casting it as part of creating the glyph. The spell must target a
single creature or an area.
There are no other limitations.
Since spells that target "self" only target a single creature explicitly they meet the single-target criteria.
Targeting - specific beats general
One might wonder how a "self" spell would be targeted upon the glyph being triggered, but the spell covers that as well:
If the spell has a target, it targets the creature that triggered the glyph.
Does a spell that targets self have a target? Yes. So, according to the spell that self spell will now target the creature that triggered the glyph.
Specific beats general. So this supersedes the restriction that self spells only be able to target the caster.
In order for this spell to function as designed, it necessarily supersedes the normal targeting rules for spells with its description.
It's worth noting that this spell also necessarily supersedes several other major general rules (Spellcasting effects, concentration) with its specific effects in order for it to function.
Thus, there is absolutely no reason why this isn't fully allowed.
The spell's wording has changed
It is worth noting that an older version of the spell description began with the line:
When you cast this spell, you inscribe a glyph that harms other creatures.
However, the spell has been the subject of errata, and the first line now says:
When you cast this spell, you inscribe a glyph that later unleashes a magical effect.
This appears to be a confusion point.
Best Answer
You Probably Can't Do This
The meaning of "prepared spell" can be confusing: like "attack" or "action", it is a term with flexible meaning in English, but also a fixed technical meaning in the game. Usually, it means a spell which is selected by members of certain classes at the end of a long rest, and is thus available throughout the day to be cast via spell slots. At first glance, this implies that spells cast via Magic Items are not "prepared spells."
But this is complicated by the fact that Glyph of Warding is on the Bard's spell list, but Bards do not "prepare" their spells in the sense stated above. So you might think that "prepared" spells could apply to any spell you are ready to cast.
That being said, a notable distinction is drawn between spells that are "prepared" and cast from a magic item on page 201 of the PHB.
In this text, we see that spells which are "prepared" are "fixed in mind." We also see that spells which are "fixed in mind" and spells cast through a magic item are two different categories.
Although this doesn't settle the debate definitively, it does highly imply that spells cast through a magic item are in a separate category than those which are "prepared." And since Spell Scrolls are considered a Magic Item (DMG, p. 200), it is likely that spells cast via their use could not be stored in a Glyph of Warding.
But...
Naturally, your DM will have to make a ruling. They could be convinced that the "prepared" term in Glyph of Warding's description refers to how the Glyph "prepares" the spell to be cast when triggered. Or maybe they might just figure that Glyph of Warding already takes so much planning and foresight to use (an hour of casting and 200 gp in materials) that it won't make too much difference if you expand its use to spells cast via magic items.
The rules don't lay out an unambiguous path, so each DM will need to decide. But the only guidance laid out in the rules does suggest that your proposed strategy is unlikely to work.