As you have found, shot blasting is one of the best methods to reveal the slivers.
Perhaps you could ensure that the grinding / wire brushing leaves an abraded surface of e.g. Swedish 2 1/2 such that the first coating would achieve a bond. This is an acceptable method during localised repairs to paintwork.
Check your paint spec and see what are the minimum requirements for repairs, that may give you a clue / answer.
Dye pen would be messy and time-consuming in that you would need to de-grease and if you are coating afterwards you need to clean off all the residue (though the blasting may do this for you)& is not conducive to a production-line process.(requires dipping and tanks etc)
A form of magnetic particle exam, by passing the sections through an eddy current rig may be better. This should detect surface and slightly sub-surface discontinuities and be more amenable to a production line process.There are various aids to detection in a production line environment e.g U/V.
As in all things, finding out the the root cause of the problem and rectifying it is the real answer, as not all beams / steel sections have slivers to a degree that causes ongoing problems.
Regards, Quadswift