This is expected behavior. The exact same thing would happen if you were running SVN builds of your favorite PC games. Artmoney only works because typically no one does that; We get the game and the binary stays unchanged barring perhaps a patch or two along the way (which, expectedly, will usually invalidate existing Artmoney cheats).
There is no easy way to prevent this behavior. I think it may have worked in the old VM memory model that PCSX2 0.9.5 and earlier used, since it requested specific address ranges for its PS2 memory maps. But that was also directly related to why the VM memory model needed admin permissions and liked to give us all lots of headaches and tell us we didn't have enough memory to run the game. So we won't be re-implementing that into VTLB.
Now keep in mind that while the PS2 memory may move around, the contents inside
that memory block will be consistent between revisions. This is how the PCSX2 patches system works. You specify addresses inside PS2 memory space and PCSX2 translates them and applies them based on where the PS2 memory map is allocated (which is at the discretion of the operating system). It would be trivial for us to display the base address of the PS2 memory map in the console, for example, and maybe that would be useful for managing cheats. (tho probably not)
It would be useful to me as a debugger tho, so I think I might do it anyway.