the hoses with the screws in the end of them...? They would appear to me to be part of Kawi's "egr" valve...that looks to have been eliminated on your bike. At least that would explain 2 of them.
Or Kawi may have left hoses in place to make the job of syncronizing the carburetors easier. I've not had a 95-97 zx6r apart in front of me.
On some Kawi models I've worked on, like the zx7, there was a air valve in ram air system that was tied to the carbs, which also had a vacuum line going to it....not sure if your generation of zx6r had that or not.
As long as they are sealed well, it shouldn't be a problem.
The tubes in the middle of the second picture, tied together with a "Tee" fitting need to tie into the air box or intake snorkles some where. Those are for the float bowl vents and need to see the same pressure as the air box.
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