Don't think it will make any difference really. If you have runs of ducting within the cabin the heat escapes to the cabin anyway. If you have a run outside the cabin the loss will be marginal unless it is very long in which case I would resite the heater.
The real issue is not letting the insides of the lockers get too hot so you can store things inside them without risk. We have found this pretty important. We insulated them but can't now remember what with I'm afraid. Eberspacher dealers have recommendations of course and others on here might too.
I bought some thinsulate insulation 2m wide on a roll off eBay. This is similar stuff to that sold by heater dealers at vast price.
We sleeved the air ducting with it and sealed the joins with self adhesive aluminium duct tape. Our heater has a 3m run through the cockpit locker which was getting very hot, now it barely gets warm and hot air from ducts in the saloon is much hotter
I talked to Eberspacher about this at the London Boat Show and they recommended a material. Looks a bit like neoprene foam tubing but is heat and fire resistant, quite bulky, suggest that you ask them.