By responding to a "thank you" with a "no problem" you are implying that there was a problem in the first place, amirite?

No, I would argue that you're simply stating that there is no problem in general. Like, it wasn't an issue or problem for you to do whatever you did for the person.

No problem

However the secondary definition of problem is ‘a thing that is difficult to achieve' so in that respect you are just saying ‘it was easy'

Thankyou.