I'm still learning things about this case-modding business, and I tend to limit my actions to old ATX discards. Probably why I sold my CM Wavemaster instead of cutting it up.
There's no problem, essentially, with putting blow-holes in the top and installing fans. However, my own experience with side-panel and top-side blow-holes is that they transmit noise -- even if only air-turbulence and white-noise -- in a direct line to your ear or someone elses.
If it were possible to pop-rivet some sort of shroud to top-side blow-holes and fans, they would be better. If you run them at lower rpm, that, too, would be better and you might not hear them.
Such things are not totally irreversible; you can replace entire sheet-metal panels, and sheet-metal is pretty cheap, as are a handfull of pop-rivets. Maybe a mig-welder would come in handy. But for that case -- be sure you plan to live with the results.
[And thank God my sister-in-law's computer case sits under her desk. She now has one of those top-side blowholes. I wish I'd left it alone, but "she's happy . . . . she's happy . . . . "]