Removing your filter is a personal choice, honestly.
After your NPT matures, there isn't a need for one. Your plants *do* become your filter and they're basically starving the BB of any ammonia that they used to utilize. So, in short, the BB will die off anyway. I've kept my filter on my tank because it cost me like 25 dollars and as a college student, I'm not just gonna let that go to waste, haha.
However, my newer 2.5 gallon NPT doesn't and never has had a filter. I'm one month in and I haven't had an ammonia reading yet so I see no use in getting one.
As DefStatic pointed out, the filter does still have some benefits so it's really just up to you.