If the batteries are not doing anything (Charging or discharging) 12.6 indicatges FULL CHARGE, nothing wrong with that.
Your trips to the single digits (voltage wise) on DEEP CYCLE batteries generally cost you overall life span and perhaps a small amount of capacity.
On Starting batteries, including MARINE/deep cycle, two trips that low will likely cost you ALL the remaining life of the batteries.. One of the reasons I'm pro GC-2 is that fact.. Like you I ran my original batteries down a bit low several times over their 9 year life.. had I not they might have made 10 or 11.