The boots are good for protecting your anodized stanchions from getting scratched.
But they're also good at trapping dirt that's near impossible to get to on a regular basis.
Manitou's Evil Genius seals are supposedly a cut above the old seals, but a better option may be switching to a set of $20 Enduro fork seals, which have worked great for me on my X-Vert and previously on a Judy.
Without the boots, you'll have easier access to your dirty stanchions to wipe them down after a ride, but you'll need to worry a little more about keeping the stanchion surface from anything hard enough to damage it.