It sure wouldn't hurt. Some folks have managed to discover they can get their Samson S-1000 to clip a bit before the limits of their sub driver. Keep in mind this is very much a fequency/amplitude dependent thing.
I personally feel the cost/performance of the S-1000 to be a good match for the Ultra, but having too much power is nearly never a bad thing (unless you don't know what subwoofer calibration is all about).
So if you can get a good deal on the bigger Samson go for it.
Does clippping hurt the amp if it happens a little?
I was watching the new Triple X movie and the scene where there is an avalanche it was at reference and the amp was clipping "flickering" a little during the scene.
Which amp? Some amps (adcom) have lights that flicker at 1% distortion, close but not clipping.
Typically clipping is easily recognized, you will know it when you hear it, usually it generates heat that damages voice coils on the affected drivers, some amps tolerate more clipping than others but usually you fry the speakers first. Uncontroled clipping will destroy the amplifier and speaker.Most amps have protection and will shut down.
You mentioned clipping in a triple X movie, I thought you meant a triple X rated movie, I thought that must be some movie. . .
No that shouldn't matter. If it's the Samson, a flash of that light now and again won't hurt a thing.
Now... if they are on more like a second or two, and/or you have run into excursion limits of the Ultra driver (usually accompanied with a loud "CLACK") then I'd revist your SPL calibration with a trusty Radio Shack sound meter ;^)
Assuming such is not the case, I'd not give it another thought. Checking your calibrated levels with a good test disk like Avia or Video Essentials periodically is never a bad idea though.