I don't think it should cause too many problems. That said, I don't know what you're going to do with the backups. I guess if you know how to reconstruct the database and sharepoint from config files alone, then they would be useful. We ran into a similar issue this summer with a standalone SP server. A VSS copy would have been pretty much useless and we didn't want to pay for a real backup solution. But, we are a vmware partner, so the solution was actually pretty obvious.
Too bad VSS vmks aren't bootable