I have h-s-h too , and that's how Steve Vai's guitars are set up , he oftenly uses the middle S ... It's usefull sometimes , I can get a surf rock like tone using combination of bridge H and the middle S.

Why do you want to cover the hole ? Is it for the "look" reason ?! I don't think it's so important.
You can get some plastic piece and cut it to fit in , paint it to yor guitar's color , and use an adhesive ... BTW, some adhesives may damage your guitar finish , better be sure of what you're using.

I think that your reason to disconnect it is cuz you never use it alone or by any combination with other H's , so that you can hav a 3-way toggle switch instead of 5-way , which will make you able to do the "flick toggle switch" trick, if you have 2 separate volume knobs.

If that's the reason , just buy a 3-way switch and do the job ... If you're not familiar with elec stuff , get a tech to do it for you... You won't cause any permanent harm if you tried anyway (unless you burn yourself with the soldering iron ;) ).