No changes were made to standard or STF Borg enemy NPCs alongside Season 7. A few new ones were added for the Into The Hive STFs, but their addition has had no impact on the abilities of their allies.
Plasma DOTs have always had 100% shield bleedthrough, and high-damage torpedoes have always been a difficult-to-balance issue (to put it nicely).
Borg damage was not increased.
Borg abilities were not beefed up.
That said, it's possible that Borg encountered in Into The Hive are set to a higher level than they are in other STFs. I haven't checked to be certain. But if they are, that means they are rolling on different (higher) damage tables.
I have noticed for a couple of weeks now that sometimes MY torpedos are just circles, (I have a medium-end card GTX 570) Question: Could the Borg torpedos be doing the same thing and just be REALLY hard to see when they are hitting you?.