That's actually an interesting question, and one which even comes up in judo circles. I guess the real answer is that udegarami (the Kimura) and sankakugatame (omoplata) have always been considered elbow locks in principle, so they're considered to be such in competion by the IJF as well, even though 95% of the time they're actually shoulder locks. Both are common in international level judo, so IJF level referees (the highest refereeing grades) obviously interpret them that way. There are in fact referees at local tournaments who will penalize omoplata because they feel it's a shoulder lock - an interesting example of where less experienced refs make a call that would be considered incorrect at higher levels, but which actually is probably more in line with IJF rules. Having said that, I like using both, so I'm glad they're officially allowed
In practice it's impossible for the ref to know if the competitor is feeling it in the shoulder or the elbow (people with very flexible shoulders bend until it catches at the elbow), so they give the guy applying it the benefit of the doubt.