Can I just plug the extra one off, or have I screwed up and need to tear stuff back out and redo something?
No & No
http://www.partzilla.com/parts/search/Honda/Motorcycle/1998/GL1500C+A/AIR+CLEANER/parts.htmlLook on this, it will give you an idea of what to look for.
Only the Honda Engineers know why the system is designed as it is, my guess would be for air equalization.
You should have the tube there, must just be hiding on ya.