A quick googling reveals...
1 3/8oz of steel BB contains 99 pellets.
1 5/8oz of steel BB contains 117 pellets.
So 18% more. Is it significant? Pattern your gun at various distances and see for sure. Long, narrow shot columns tend to produce less effective patterns that are more subject to stringing. The classic example of this is the 410 and how notoriously difficult they can be to master wingshooting with. Similarly, though to a lesser degree, the 3.5" 12 ga will naturally have a longer shot column than the 3" and that could lead to less uniform patterns. All you can do is shoot all the different shells you're considering, through all your available choke tubes, and see what patterns best at various distances. It will be a long process, but ultimately in an afternoon of shooting and pellet-hole counting, you should come up with a combination that works for your hunting area and style.
Taking advice from me, who only pass-shoots geese in Saskatchewan is completely irrelevant if you plan on calling in ducks over decoys around a slough or in a wooded swamp.
For me a 3" or 3.5" BB is exactly what I want in my Browning Gold 3.5", but there are times when I'm chucking a 2.75" of #2 Bismuth or Tungsten-Matrix out of an older double.