If you don't use the grease, everything will still work.
The grease helps to repell moisture and keep good electrical connections. I would also assume that the boots will come off the plugs more easily in the future with a little grease in there. It really sucks when a boot tears when you're checking the plugs or something.
I also highly recommend anti seize grease on the spark plug threads.
a friend of mine has an msd setup, and when it would rain he ocassionally heard a pop then he had a misfire. he'd open the hood and an a wire would be off the cap. greased the boots and it went away, only thin i could think of was moisture got under the boots to the connection and had some steam power going on.