Let me give you a generic answer:
If it as much as touches the HDD during the relevant time period, then yes. In that case you should also change file system to f.ex. Smart File System (SFS), if you're still using FFS that is.
But then again, a 68060 accelerator is very expensive. Not to say outrageusly expensive, considering actual performance. I would give you bad advice if I didn't tell you to have a look at the x86 option first.