I prefer to go Biscuits for the mana restoration in the early game as Thresh can quickly eat through his mana pool and the health regen is also quite nice as he has no sustain against poke.

Hexflash is still a really good rune though if you can access the bushes in lane (or stay behind walls) to hide the channeling animation. It also gives added mobility around the map as you can Hexflash over walls.

I think it's mostly personal preference, if you don't find yourself wanting more mana then Hexflash is certainly better as it gives you more opportunities to make plays.

Thanks for your comment! Hope my answer helped ^^