Depends what your inspection covers. Getting deleted and then tuned will result in readiness lights being disabled, which will throw a failure if your state checks readiness. If they do any form of smoke test or opacity test you could potentially fail that too.
I'm pretty sure the tune takes care of making the vehicle show readiness. I can't speak to MA but NH plugs in cars to the OBDII as part of an emissions check and tuned vehicles pass here.
Emerscape, my take is that if you just want a tune you are probably all set. If you're planning to delete anything then you could easily get busted on a visual inspection (which is the case here in NH as wel).
I can assure you, if you delete anything (dpf, cat etc), the tune will blank out the readiness. A true emissions scan will show something is wrong with the readiness. Every state is different.. some don't emissions scan diesels, some allow up to 1 or 2 readiness issues, some will instant fail if there are issues with readiness.
Regular tuning with nothing deleted won't cause an issue.