Some of the architectures also have different endianess and incredibly complicated peripherals to the cost effective host machines as well meaning that it's actually more power efficient to run native. A headless 100MHz VAXstation for example draws less power than the equivalent host that would be required to provide a full, accurate emulation with peripherals. These aren't arcade machines.

Portability issues is where real hardware benefits. It's where you have battles of unusual register sizes, endianess, host/network order differences, different memory models and memory protection, different performance characteristics, different timings and different exploits.

Unless the emulation is 100% accurate, including timing, which is a really difficult thing to do (look at the effort MAME goes to), then the benefits over real hardware is moot.

Emulators are also expensive to write due to the above, have their own bugs and don't always recreate the bugs in the real hardware (which are sometimes exploitable).

Also, using emulated hardware could cut down the usage of the real pieces, which could then be better studied and preserved. Doing less builds on vintage hardware is, actually, a good idea.

Then again, it's possible that emulation could surface other edge case issues. That's completely orthogonal to the value of non-emulated archaic architectures for this purpose, however.