Alternatively, for an entirely "black" approach using unregistered, unmarked and possibly undetectable ships, they might just use a teleporter -- stuff like this is rare tech, but considering the crazy weapons the operative is equipped with, it's actually pretty tame! The graphic novel Daemonifuge could be an example for such an incident.
To be honest, teleportation also makes sense specifically for a Culexus - after all, the usual problem is protecting the teleportee during a shunt through the warp; which is why it's usually restricted to those in terminator warplate and the super-psychic warded Grey Knights. A Culexus is not exactly going to care about being shunted through the warp either; in fact he's the only vaguely human individual for whom the experience could ever be described as 'boring'.
The Nemesis covert kill-ship did have a navigator, I believe, but the navigator was itself servitor-ized - something the Navis Nobilite wouldn't take kindly to, but it's not like the Assassinorium is noted for (a) following the rules or (b) being nice .