I had boots on mine for a few years and never had a problem with stuff getting inside and causing any corrosion. But.........I really never put the truck through too much of anything to get crud and other stuff inside the boots. If there are small holes at the bottom of the boots then water won't be a problem. If you go through a lot of mud then they could get clogged up and start corrosion on the shafts.
If you like the look of the boot on, then leave them on. Just check them after some wheeling in mud/water once in a while. It doesn't take that long to cut off the tie strap that's holding the boot on, then replacing it with a new one.
The new bilsteins I have now don't have boots on them and I don't plan on putting any on. I like the look without the boots but that's just me.