Class mods bypass the 5 skill limit.
Most skills are bypassed by Class Mods. However, in some cases you may not wish to go beyond the normal limit. Once such example is the Hunter's Trespass ability. When maxed (5 points) it gives a 100% chance to bypass the shields of an equivalent level enemy. Adding extra points to this skill when maxed at level 50 becomes redundant due to the fact that enemies only go up to 52 at the most.
There are other skills which are highly benefited by class mod bonuses though. Once such example is the Beserker's Short Fuse skill. This skill reduces the cool down of the Beserker 6 seconds per point. The normal beserker cool down is 60 seconds, so maxed out at 5 points the beserker will have a 30 second deduction. However, if a Skirmisher class mod with a +4 Short Fuse line is found you receive an extra 24 second deduction. This brings your total deduction down to 54 seconds and your total cool down time to 6 seconds. In other words, with 9 points in Short Fuse you can Beserk until you run out of time and then Beserk again 6 seconds later.