One thing I've got to comment on, BC is right about it making a lot more difference at that bbl length than at others, but his observed drop of 120fps is pretty conservative, I've seen drops of 300fps going from a 20" to a 16.5" from a .300WM, the .30-06 I tried did about the same, a ~250fps lost...

Just figured I'd point that out, since 120fps on a .30-06 is only like a 4% loss, but what I'd seen was around a 10% loss. It really just depends on where your load's "sweet spot" is. The sweet spot is really the point where the bullet reaches its maximum velocity, OR, where its acceleration levels out...at first, the bullet is going to be accelerated slowly, then very quickly it will begin to accelerate VERY quickly, then eventually it will level off and begin to decay again. The sweet spot is where it levels off. Drop bbl length below that point and you start cutting out a LOT of power.

That said, I don't really know that I'd worry about losing 10% of my power from a .30-06, heck, even at 10% velocity lost, it's still going to have around 2200-2300ft.lbs of energy (about what it'd have at 100yrds is what it now has at the muzzle), which is still more than a .30-30 has at the muzzle!!!

Truth be told, it may be possible for a handloader to achieve nearly identical results in either bbl, as long as the sweet spot isn't too far ahead of the muzzle, just by changing powders. Loading a faster burning powder might let you bring the sweet spot back into your bbl without increasing your pressure beyond the rating of your rifle. You might look into this should you decide to go ahead and chop your bbl.