Like Tony said, rationale for removal is to keep the bike from running too lean and therefore hot... especially around the exhaust valves, which don't have a stellar reputation on our bikes. I also found that the right hand pulse air pipe kept my right carb bowl from coming off.
BMW sells a screw that threads into the vacuum ports. I prefer to use them because rubber vacuum caps tend to get brittle pretty quickly, and then they can start leaking. Also, if you ever end up with an intake side backfire, it can blow the rubber caps off (it happened to me once, though I don't have the rubber valve in my airbox).
I use rubber vacuum caps to cover the screws, both because they keep the screws free from grime and I'm paranoid that the screws will rattle out.
You'll also have to somehow seal off the airbox where the vacuum lines go in (fill the hole where the T goes, cap off the T, etc), or you will have an air leak downstream of the filter.