You can find replacement Shimano brake hoods for aero levers at loosescrews.com or biketoolsetc.com, but I've used brake hoods from other manufacturers on Shimano (old 105, from 1987) levers, and that's worked fine. You can usually find Dia-Compe aero brake hoods on eBay. I used the extra set of hoods that came with the cheap Tektro-made aero brake levers that I got for $15 from Nashbar.
I've also removed brake hoods from Shimano STI brake/shift levers in order to soak them in solvent and get the rachet mechanism working again, and I put the rubber hoods back on.
I didn't need to grease the brake lever bodies or anything, in either case. And remember that if you do that (such as using WD-40) then the hoods may always slide around a bit on the lever bodies, and that's something which would be annoying while riding.