I don't think it's so much case-by-case as it's the fact that one isn't really smellier than the other?
As long as you clean up, you really shouldn't have any issues, especially with just two.
I'd say go with males if you wanted to avoid surgeries though. Males don't always need to be neutered, you only do it if someone gets overly hormonal. But the chance of an unspayed female getting a mammary tumor is much higher than a spayed female (I think it's something like 49% vs 4%). Spays are more invasive, risky and often expensive than neuters also.
For the shelf, I would use corroplast (
like this) personally, because it's sturdy, reusable and easy to clean. ^_^