This is a good point, however filtered pipes are specifically crafted to smoke well with filters. I still find smoking filterless more enjoyable personally.I always draw on the freshly packed bowl to judge the draw before lighting. Many times I get a small piece of tobacco that pulls through, but never any after that. I am careful to never stir my tobacco at the end of a bowl (I will gingerly dump if necessary) to avoid the ash, and then I never get it. The only filter that I want to taste is the tobacco in the bowl. A filter will change the taste and the smoke. We strive for the perfect blend, why add a flavor?!! We strive for a straight and open stem to avoid condensation, why disrupt the flow and virtually guarantee it is not laminar - even if the filter does not allow the moisture all the way up the stem? Why put a plug in the way so that I can't pass a pipe cleaner? And finally, why add complexity and expense?
After all that, use a filter if you wish. We all enjoy the routine of smoking differently and you do what is best for you. I personally avoid filtered pipes for all the above reasons.
Concerning moisture in a filtered, you must remove and replace filter as well if you are going to smoke half a bowl and then leave the rest for later. Another hassle you don’t have to deal with non-filtered pipes.