Whether or not Astarion has a soul wouldn't affect his ability to make a deal with Raphael because:
Raphael doesn't ever ask for it. What he wants is for you to kill the Yurgir and, at least in my playthrough, my character refused to kill the Yurgir without Raphael agreeing to read Astarion's scars. The deal had nothing to do with souls.
Additionally, Raphael considers you to be the most important deal of his lifetime if he's ever to get The Crown. So him showing good will is a manipulative tactic on his part. Not every agreement with a devil is for the soul of another and he wants yours much more to get the crown than to add another soul to the roster. So he may not ever want anything from Astarion other than to get into your good graces.

Also, there is mention if you take the deal with Raphael for the hammer, Astarion says "I would never sell my soul so willingly but hey, then again, it's not my signature on that page." so, whether or not he has a soul, he certainly THINKS he does which might be what Larian is doing with him.

#JusticeForAstarion