No idea but you are right. Boylan, Ashe, and Pullen probably have low clearance, but that is just a guess. I do not think that undercutting would be possible due to the proximity of the wye at Boylan and the NCSU tunnels at Pullen. Maybe undercutting could be possible at Ashe but maybe not. The two in Cary at NW Maynard and Cary Parkway are pretty new, as is Gorman, so they are probably okay.
Some of these bridges were actually planned for rebuilds as part of the failed 2005 rail project, not necessarily because of vertical clearance, but rather because they were not wide enough for four tracks plus the NS-mandated buffer. However I am sure that if they were rebuilding the bridges anyway they would certainly go ahead and build in enough clearance for double stack under wire. I specifically recall that Pullen and Gorman were planned for rebuilds. Not sure about Ashe. Boylan was not on the list. So that means there are some stale 15 year old engineering plans lying around somewhere that could be dusted off for some of them, if it ever came down to it.
Not sure about anything south/east of downtown like Kindley, Wilmington, Hammond or I-40. I really dont know, this is all just barely more than baseless speculation.