I have restarted my game after finding out that Tarquin was supposed to appear at Stonegarden but never did. On my new game once getting to Act 2 I started to monitor the situation more closely by going to the Stonegarden time and again to see if Tarquin is there.
Then after investigating the house of Mordus in Driftwood, and also solving the disappearing Magisters quest, I went to Stonegarden and voila, he disappeared. I reloaded a save before going into the house of Mordus and found that Tarquin was still there. I could not do further testing because it was getting late and I needed to sleep...
Anyway, it seems something is messing with the triggers of Tarquin. I have heard that going inside the Lady Vengeance may have to do but in this playthrough I have never entered the ship for respec. I have also barely started exploring around the map, only doing the quests in Driftwood.
I really, really hope the upcoming patch this week can solve the issue of this quest (along many others).