is it ok to delete the old version, I don’t want to lose any of my settings after moving to the subscription
Settings are stored in the user Library (~/Library) and are not part of the application package. Deleting the application package will not impact your settings. If you use some kind of uninstaller software that looks for files beyond the application package, those have been known to wipe out preferences. I would recommend just moving the old version of Photo Mechanic to the trash.
If I download the new subscription version does this automatically replace my old perpetual license version
No, it is a separate application.
If you install it on a Mac you will have a new application called 'Photo Mechanic' alongside the application for the older version (likely called 'Photo Mechanic 6' or 'Photo Mechanic Plus' on your system)
My old version ran on my M3 IMac in emulation mode, will the new version automatically run in Native Apple Silicon mode or do I have to change any settings.
When you run a Universal Binary application (which is what Photo Mechanic is) your system chooses which code to execute. Unless you specifically force it to run on Rosetta (which you have to go out of your way to do), it will run as native Apple Silicon code.
Will I get a new license key with the Subscription version
Yes.
in the future will the emulation mode stop working?
Only Apple knows the answer to that question. I would recommend looking up how they handled the transition from PowerPC to Intel, and how they handled the end-of-life for 32-bit application support, for their track record on similar types of transitions.
