The ditching aspect is not very significant; more important is the flight planning, on some types.
e.g. On the 76 you need to enter the Cat A graph 1000 ft above T/O altitude, which has some impact. Aditionally the TAS/FF ratio will change significantly.
Even on types with low drag gear, such as the 332 there will be some effect (maybe 5% more fuel). A few years ago a certain UK operator had a gear collapse on a diversionary landing; the gear was selected up after T/O but did not retract. This was not noticed, but the reduced TAS/increased fuel burn was and the diversion made due to low fuel predicted at destination. The gear collapsed on landing with the selector still up (lots of CRM issues too, e.g. checklist use).