I've been noticing that that comics prices don't actually reflect the number of pages with story in a book (i.e. check out $2.99 books to $3.99 books). The rest of these pages are, for the most part, in house ads for other books or merch. How come the comp

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I'm not 100% sure I understand the question, but let me see if I can hit close to the mark for you. If I'm missing something, I apologize.

Page count is only one factor in pricing. Factors like the creative expenses (it costs more to have Bendis or Morrison write a book than Joe Newbie), paper quality, and other things. Also, the popularity of a book may change the price, ie. Marvel charges more for some of their more popular titles, to make up for the lower profit on the lower-selling books. They may also sell newer books at a lower price point to entice new readers.

So there are a lot of reasons. At DC, generally, all the books are 2.99 regardless, UNLESS they have a higher page count. I prefer that, I admit, it seems less arbitrary and more reader friendly. But I don't really know all  the reasoning for Marvel's prices and they may make perfect sense when all factors are considered.

As for ad space, condoms are probably not going to ever be in an ad in a Batman comic. And the ads aren't chosen by the publishers, not in the way you seem to be implying. The ad pages go to the clients who order them, not necessarily to who the publishers might HOPE would take them.

And I see ads for licensed goods all the time. I just grabbed a random Batgirl comic and the first two ad pages are for a game and tv show, both licensed DC properties.