I think there's a big difference between pausing to pause, even in the midst of a pattern, and pausing to supplement/replace reaction time or reading ability. In Touhou in particular, it already tries to dissuade you by blurring the screen, and many other games do similar things so you can't pause buffer as easily.
If we're talking about things like DS speedrunning, then I wouldn't say it's a problem, as manipulating everything possible about the game is a core premise in speedrunning and TAS. For regular play, I don't really care, just as with any other "way" to play. I have a bit of a problem with claiming to have completed some common goal (i.e. scoring, 1cc, etc) as though it were on the same playing field. It's really grey, especially since safespotting seems similar in ways, but I think explicitly trying to cheese something using a game's auxiliary features rather than taking advantage of what's offered in the gameplay, is at least morally worse. I can't really think of an accurate comparison to make here.