What a coincidence, I saw your message when I was about to upload 1RL v1.1 which integrates your previous suggestions (and corrects the typo in "invokes"; the complete changelog is here).
You are right: the weakness of bugs doesn't trace their creator but the current equipped features. It's a detail but since this would make the rules more consistent, I fixed it.
My idea was to make the profiler more useful when overwhelmed, since the time penalty is so huge that the duration difference between the printf() and the profiler becomes negligible. Since the profiler is clearly more precise, it would yield in this case a higher DPS. I may balance it later (by making the profiler faster or even more precise).
About the hack bug, I may have found it. The inventory is not refreshed when a feature is made less stable because of a hack use. It may explain the behavior you encountered. But it probably needs some balance too.
By the way, I reworked the confusion mechanism. Previously, missed attacks with a paradoxical weapon had 50% chance of confusing the enemy, which made the paradoxical hack and its 100% accuracy useless. Now, successful attack have 33% chance of confusing the enemy. The confusion last longer (when you told me the confusion didn't work on the invoked bugs, I guessed that the confusion duration was just too low w.r.t. your time penalty, so the effect was nearly invisible) and confused bugs you attack have now 50% chance of refocus (I might tweak it later).
Finally, I would like to say a big THANK YOU for helping me enhance the game and increasing its visibility!
Edit: 1RL v1.2 is available :)