Omsi will start up a little faster because it has less content to scan when it starts - instead of looking through perhaps 15 or more map folders for global.cfg files it'll only have to look through 1 or 2 for example. It won't change the performance actually in game because the map is going to have the same stuff loaded and it won't affect loading times of maps at all.
It does add a bit more reliability perhaps, when I install a map it'll be into a new clean copy of Omsi so it won't overwrite and break anything else and if I want to uninstall a map and it's associated content I just delete it's Omsi install instead of attempting to work out what it did and didn't install.
Alongside the different installs for different maps, I also have installs for different purposes. I have a dedicated Omsi install for developing and testing the C400 for example; with only it installed there's no way I can rely on some random file I've downloaded from the internet. For my dabbles in map creation I've used my dev install, being separate from other installs I can have only my own content and a few select other pieces installed so I know that what I'm placing on the map is something I can either include in a download or easily link to as I know where it came from. If you develop on the same install as you install a bunch of different maps on, who knows where half the stuff you could potentially place came from. I also have a test install which I regularly sanitise and reset, useful for testing stuff in the approval queue because it immediately shows up when someone has failed to include or link to a required file because if it's not a default file I won't have it on that install.
If you try something like I've got with 16 different Omsi folders, you'd likely find that your hard drive is suddenly a lot fuller than it used to be, because you're duplicating a lot of things. To this end I have abused
symlinks extensively, meaning the total size is only 55 GB, which seems large but given a clean Omsi install is 4.3 GB, is still less than having that many clean Omsi installs.