Not a cuemaker, but I've done a bit of research on snooker cue making, and here's what I found concerning filling the grain.
Mike Wooldridge uses a slurry of oil (boiled linseed oil I would assume, but he keeps the ingredients secret) and ebony sanding dust, which he rubs into the grain. This process is repeated several times over the course of days or weeks, buffing with steel wool in between applications.
https://handmadecues.com/finer-details/ (scroll down a bit just before "Eyesight" section).
Andy hunter does the same, apparently with raw linseed oil.
https://www.youtube.com/watch?v=GQ0Zrz-f_tA
As the oil polymerizes, the dust will fill and stay in the voids of the grain and give that distinct look at the same time.
I don't know if that technique can be applied with non-oil finishes.
But as Kim Bye said, mass production and the majority of better quality hand made snooker cues use colored grain fillers.