Clay?

I looked at your cage plans and got the pegboard for to make a ventilation area, but was wondering why one could not drill holes direct into the plywood backing instead of using the pegboard?

You can, but it will most likely look like crap. Unless you are especially skilled with a drill and layouts.
It's hard to get that grid pattern to line up through several rows.
I like the looks of the vent too, particularly when the pegboard is painted black.

I use the pegboard because there's no way I'll get that grid perfect by hand, plus it's a lot less work compared to the $10 for a full sheet of pegboard, which is enough for many cages.
When the vents come to less than a dollar per cage using pegboard, I can't see investing the hour or more to drill my own.

OK, pegboard it is, OK to use latex or does it have to be oil if I want to paint mine black also?

Latex will be fine for the vent. I think I used flat black rustoleum paint actually because I had some on hand. I like the flat better than gloss for that purpose.

It did occur to me that you could use the pegboard itself as a pattern to drill holes and avoid the problem getting them lined up. Clamp the pegboard to the cage piece and drill through the existing holes.
Of course you have to have the pegboard anyway to do this, but it's a thought. You can buy small pieces of pegboard at Lowe's and not have to get a full sheet.
I still like the final look of painted pegboard better myself, but if drilled holes are what you wanted, this would be the best way to do them.

Actually, the backs are 3/4" plywood and I was not confident in my ability to put in perfect looking vent openings, but I got some scrap lumber and am going to practice (same with the router I got just for this project, I am going to practice on scrap first).
I think rather than running away from doing it the right way, I will just practice until I can do it. When this is done, besides beautiful snake cages I will have a whole new set of skills!

Just a thought here...

I usually use plastic laminate over wood instead of painting it for cages that aren't going to be made of hardwood and stained to match furniture... Even then, I usually use plastic laminate on an enclosure, then build a hardwood piece of furniture around it. You can easily incorporate a heavy gauge wire mesh (not thin like window screening, a thick, solid ridgid wire that doesn't bend easily) by stapling it over the ventilation cut-out prior to adding the plastic laminate, which the covers the edges... a small strip (or four, depending on the shape of your cut-out) layed sideways and a little silicone aquarium sealent under the edges will ensure you don't have plywood or MDF open to water and it gives a very finished look.

Just a thought of course, since this means a different finish than you were planning.