It's not a big deal, but it is annoying and an incentive not to update the software.
I have the same issue... it's really not a big deal, and I'm
sure there are bigger fish to fry, but it is slightly annoying.
Another option might be to change the NSIS script so that it does a IfFileExists before a CreateShortcut, that would at least fix it for me if it didn't overwrite any custom options I've added to the shortcut in the Start menu on Windows.
(But again, it's a pretty minor thing....)