Am I hurting my speakers?

I have a pair of Yamaha NS 1000M speakers that are rated 50w continous and 100w maximum, and they are being driven by a Creek 4330R 40W amp. I think they sound nice, and have not heard any distortion on my tweeters. I think the amp is rated at 40w idle and max 200w. Am I okay or am susceptible to clipping, and would I even hear it?
Your probably fine...the difference between 40w and 50w is nominal...these are only manufacturer's "guidelines"...if u listened at high volumes that might be an issue...but like you sounds good...contrary to what many think...normal low-level listening takes very little power...often under 10 is only for very dynamic music at higher volume that requires more juice...or speakers that are very inefficient(to obtain reasonable SPLs)..happy listening
To give you a further idea how watts per channel compare on paper: To have an amplifier that will play twice as loud as your 40 watt amp; you won't need 80 watts, you will actually need 400 watts.
I can't say. What music do you listen to? ; )
Well I listen to rock and jazz. And someties a like to get on it somewhat, but rarely more than 60% of my volume dial.

Would I hear it clip or not?
If your not hearing it now..dont worry about it...and yes...when Solid state clips...u would hear it...
I bought a pair of ns1000's new in '81 and have been running them with a threshold cas 2 (100w/ch) for 20 years including a bunch of parties in college in the early 80's. No sign of damage so far!