Not sure if that is a bug or feature. Everybody in a larger team must have faced that issue already if working on a common model.
I consider this one of the worst, or at least the most dangerous, features in EA.
Whenever I meet a client who's discovered the Hide Connector feature, I always advise them to get rid of it as a practice, the architectural reason being that it's purely a GUI feature which encourages a magical way of working where some information is simply there without being stored in the proper data structures, and the practical reason being that it is impossible to control and thus a maintenance nightmare.
The typical objection is that there is a need to describe different aspects of things, eg systems. So systems X and Y have not one but several types of relationship between them, such as dependencies, information flows, etc. To which the response is that that's fine, but it doesn't mean that a system should be represented by one single element which is reused in every single diagram. That would be a bit like saying that in all the documentation for a system, the system's name can only appear once, and in all other places there must instead be a reference to chapter X.Y.Z.
I usually get blank looks at this point.

But there are better ways to achieve the same result as hiding the connectors.
The simplest one, just a step up from hiding, is using diagram filters. Unfortunately, as of EA 11.1 connector filters are pretty limited in what information they can look at. But they do have access to name, alias, type, stereotype and notes, which is sometimes enough.
The other option is to use stereotyped connectors and shape scripts. Shape scripts have access to most of a connector's information, and a lot of information on the source and target elements as well, but they can also check which type of diagram they're being drawn on. So all you need to do is write a shape script which doesn't draw anything at all if the diagram is of the wrong type.
Cheers,
/Uffe