By thought balloons, do you mean all speech bubbles? (Not just thinking cloud-like balloons?)
With Mokuro, this is made a little tricky as sometimes it’ll join disconnected dialogue from a two-part balloon (which can be good) and other times it will split a balloon (not so good):
The split on one balloon, at least in a few examples I’ve looked at, is predictable in how one overlaps another. Maybe to the point that an update could be made to Mokuro to catch it.
