While I can't provide information on 400s specifically, I can say that I have had 'pods' on my 500/4 continually since 1995 and it runs perfectly well throughout the rev range. I did increase the main jet size and had the carbs balanced professionally with the new filters on. I also have a 4 into 1 exhaust system. It has a tiny flat spot at 2500 revs but it is hardly noticeable and it passes through it very quickly. I find the bike well behaved and simple to ride in traffic, as well as picking up very well at main road speeds.
My understanding is that the standard original setup has it's roots in emission and noise constraints, particularly in the USA market. When I bought my bike the original airbox was missing so simpler to get individual filters.
I am not dismissing that many people have endured problems with this type of setup and realise that the 400 is a different machine but I am very happy with mine and would do the same if I was building another.
Incidentally, I now have slide carbs on my CB350, Amal Concentrics with bell mouth inlet and no filters at all. This bike runs better than it ever did, slide carbs suit it very well. I know not having filters will wear it out faster but it hardly ever gets ridden these days and I have a spare engine
