i have 414 nin pen on 1 rune and it doesnt seem to make any difference in my damage against kakashi clone with no gear on, tho it could be kakashi clone has no resistance to *e

I have the same and it adds around 700-800 damage to Fire Main Phoenix jutsu.

That's right, there must be a HUGE difference for it to happen, I've only seen it happen when I fought ppl 40 lvs below me (their control on me failed) or in ninja exam where mine fails on stuff. I suspect that the fact that some people can hit through hinata with a normal attack have something to do with control or something, as that also only happens when there is a huge gap in raw power as well(mostly ninja exam again)
That said, there is a good chance that whatever amount you can get on a rune wont be enough to make a difference on any fight that's evenly matched and any fight where it's not evenly matched, it's a win more or lose less situation unlikely to change tide of battle, so it's probably quite useless. Only exception might be ninja exam PvE where the tiny chance of resist/not-resist might let you grind to win.