If you have never had probelms like this and haven't changed any of the valvetrain (ie the valves, valve springs, cam, timing chain, lifters, pushrods or rockers), than I would have no clue why it would do it.

As far as how to check if they are bottoming out, you will need to put a feeler gauge in between the coils when fully compressed from the cam and whatever the springs are rated for is what they are not sapposed to go past. It should say on the spec sheet for the cam. I forget exactly what they call it.