The DSV's crew could be Altas and slaves but there would be occasions when crew members were out of direct contact with Zen (or its equivalents), and the slave Blake meets is certainly capable of independent mental activity. (I assume that the designation 'Deep Space Vessel indicates that it was a research vessel: Zen's statement that information must be acquired not given would be consistent with this. Was the 'image device' Zen used on the persons from the London a means of keeping revolting slaves away from the flight deck?)
One issue that has to be considered is whether the System's space centre is the equivalent of a (Terran) dome or of Servalan's command base (in either case with the equivalent of Central Control integrated). It is clear from the way the Liberator 'fits into' the holding bay (including the access doors) DSVs date from at least the time the space structure was constructed (and there are at least two holding bays - as the other DSV was not previously seen when the Liberator arrived).