Yes, the overweight charges still apply, but the linear dimension limit is waived. My kid used to be a serious ski racer and traveled throughout the pacific northwest to ski races. When the races included all four alpine events, he had to take four pair of skis with him. I was fortunate enough to find a ski bag that held four pair of skis, but this exceeded the 50# weight limit and we would get charged for the excess weight.

Another consideration is that skis can get bumped, particularly if flying on Horizon. This is more of a concern for a racer, however, than a leisure skier as rentals (demo skis) could suffice as a good backup. The kids also always carried their boots on as a carry-on because it is very difficult to properly fit replacement boots.