To my knowledge, it is not possible to mod hidden WPs. As soon as a ship is in range, the WP appears. You can make a WP cloak stuff in the sector like a storm, but there is hard-code in place that overrides anything else trying to cloak a WP (like a system scope sight obscuration ability).
In the data files, we have no control over how far apart the game will connect systems with WPs, or any way to tell it to make WPs that skip past a bunch of intermediate systems. The closest we can come would be a cluster type map. With a custom map generator hooking into the map compiler utility, it would be possible.
I don't currently have any more plans. If you have any suggestions or requests besides the WPs though...
