No, really not. Well, if you had a situation where you needed to check for undesired connections, and connections don't show up on your screen, it could be kind of annyoing. However, with the features the WP editor offers, such a situation is relatively easy to avoid.
The solution you gave sounds perfect, but has low priority - especially since it's something that doesn't affect players at all, only us waypointers... *sniff*
Interesting, though, that Huntakillaz reported to have seen the problem on smaller maps... unless these maps have extremely dense waypoint systems, a too big TE count shouldn't be very likely to occure there, or can there be many TEs in the .bsp itself?