Not only do D&D vampires normally have souls, by standard, so do mindflayers.
Additionally, while vampires may be considered undead, there's no period of actual death like with other undead.
That is, to create a zombie or ghost or whatever, a person first dies, then something happens to the dead person (or just the body) to create the new undead.
But with vampires a living person is turned directly into a vampire, no dying first. So intuitively their soul would not have a chance to leave, because they didn't really die. Their body just changed.
That aside, Raph's deal doesn't ask for your souls anyway. You can take and do the devil deal option and keep your soul, because it was never what he demanded in the first place.
