Yes, the pumping cost is awkward. But this is a killer for the big servers. Against shapers corps often put 3 pieces of ice, if not more, on R&D. In such a situation the base strength is 4, enough to break plenty of ice cheaply. And if you look at the list of 5+ strength sentries few of them are actually encountered in the wild on a regular basis.
But let's face it, there will always be situations where you need more power, either because a server hasn't been iced enough yet to boost the strength enough or because you run into a rare 5+ strength sentry. For such cases shapers have some existing tools such as The Personal Touch, Net-Ready Eyes and Dinosaurus and there are events such as Lean and Mean and Injection Attack.
If you do need to boost manually however it's pretty likely that you'll only need 1 extra strength, in which case paying 3 is pretty gosh darn inefficient.
A useful side-effect of playing Na'Not'K may be that the corp will be wary of creating too high stacks of ice, though glacier play isn't so popular that this will actually happen all that often.
Overall I think Na'Not'K is an interesting breaker, with proper support in a deck it is a solid in-faction alternative to criminal breakers.