As far as storage goes, I keep my extra MVS carts inside the cabinet. They don't get really dusty inside, but it's a good idea to keep them in anti-static bags if you do that. I have a bunch of other arcade pcbs as well, and I just keep them in anti-static bags when they aren't in use. There's no attractive way to display those ones, so I just opt for protection.
As far as inexpensive carts go, there are tons under $50 for MVS. For non-fighters, they've gone up a bit in the last few years, but most of the library can be had at less than $100 a cart. Where it gets pricey for stuff not on the multi-cart is stuff like Twinkle Star Sprites, Windjammers, and the newer homebrew stuff like Gunlord or Kraut Buster. I already have several versions of Twinkle Star, but on Windjammers I just bit the bullet and paid for it. It ran me about $130, but it's a legit cart and one of my favorite arcade games.
Super Dodgeball, assuming you're meaning the arcade original and not the Neo Geo one on your cart, is JAMMA and can be had for under $100 if you watch for a good auction on a pcb. You don't have to doctor anything up to put it in your cabinet, just put a piece of thin wood on top of the 2 slot pcb to keep them from touching while it's in the cabinet and plug the main harness onto the Dodgeball board and you're done, almost as easy as swapping a cart. (assuming your 2 slot has the metal cover).