I removed the canister last spring to install the jack adapter, and after 12,000 miles I've noticed no change or ill effects. I couldn't figure out where the hoses went, so didn't plug them or anything.
Fred.
Sounds as if you have a California Valkyrie.
Since you've taken the canister out of the system there is a possibility of vacuum leaks.
My suggestion would be to complete the job and do a de-smog on your bike.
There is no downside to doing a de-smog and there is no gain for that matter either.
The net result of a de-smog is simply a cleaner less restricted environment on the top side of the motor and the added advantage on having nothing that can deteriorate causing a running problem.
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