So far (upto 10.5.6), I have not seen any problem with the software update from Apple.
In general, you can do any updates from Apple except the system update. All application updates and security updates should not cause any problem. However, when it comes down to the system update, just take precautions (i.e. backup important data and applications, etc.). In theory, with EFI install, the system update should not cause any issue, but it is not from Apple and I don't think anyone can guarantee 100% future compatibility.