When you ask whether they will be allowed in, I assume that you are wondering whether they will be allowed by Apple.
Seeing as both packages are available in the physical and online shops, it suggests that Apple are happy with the software. I understand that there are issues with the way that packages are installed which may be a problem (way beyond my expertise level).
As for whether they would want to, I'm sure both products lose a fair percentage of their sales price on marketing and distribution fees anyway, and they probably wouldn't get a lot less per copy than they do now. However, they are very much packages that are sought out, rather than impulse purchased, so I doubt whether many people would buy it just because they are available in the App Store.
Having said that, the one that got on first would possibly get a bump in sales until the other caught up. The fact that people have to buy a copy of windows may lessen the App store effect but I bought Parallels recently, but would have got Fusion instead if that had been the only one in the App store.
Basically, there are far too many unknown for the casual observer to be able to say what they will do (unless the installation issues are obviously a block).