I would disagree with one idea. No honey house should be without drive in ability. A garage door for a fork lift to enter, or a quick entrance with a pickup in a pouring rain. You think carrying supers is bad, wait until you start carrying 600 lb. drums out and loading them.
One of the catches to the planning department is that they will not allow a garage or shop or anything built on the property until there is a dwelling on it first. I am guessing they were stung too many times over the years by folks building garages and then never building the dwelling to get around the regs.
then submit the plan with a wall where you wont put them and call that space a garage, as part of the "house" you are going to build. you WILL want the door... If they have to inspect and ask where your fire wall is, tell them its going up last, so you can use the garage area for constructing interior walls, cabinets etc... Yes, ONE garage door, take Iddee's word for it! If you must, make the door JUST large enough for a trctor bucket, or a skid steer.. a large double door you can roll barrels through with a concrete pad outside of it if possible. Pallet jacks roll nicer on concrete.
The area I use to extract is not that large, but I have plenty of room around my extracting area to put supers, buckets, jars etc, etc, etc... The one thing that I have quickly found, is that the honey extracting area has also become the canning area, and the wax processing area, NOT to mention making maple syrup...... Room for storage, as you well know, cannot be overlooked. If your certain you are going to USE 1000 square feet, then make it 2000 square feet. It may be too large at first, but you will quickly grow into it. In three years you will be wishing it was larger. You know as well as anyone how crowded things can get with 100 supers stacked up.... it seems to get more crowded with 38 Supers FULL and 38 supers empty and 24 frames in the extractor....
A drain in the floor is a must have. Here, where I live they allow me to run a drain straight out to daylight/ditch which is PERFECT so that I do not have to worry about plugging up pipes with wax particles. If I had to run them through a septic I would put screens on all the drains and deal with cleaning them every fifteen minutes.... If zoning forbids a drain in the floor, put it in anyhow, and pour conjcrete over it, so you can chip it out later. Drain, yes!
Concrete around the outside edges would be perfect, Cinder block a close second. Water, and a water heater.... Outlets lots of outlets. Wait.... is this going to become the wood shop too? Seems I recall someone making boxes and cutting handles outside....
HEAT would sure be nice to keep the pipes from freezing.. if you cant KEEP it heated, install a frost free faucet and hook your water system to it. that way you can shut off the faucet, and the water will drain back to below the frost level. I have a couple of them, and recommend having it outside the wall, and hooking the hose to a camper connection or similar in the wall itself. If you ever have to dig up the faucet for service it will save you tearing up concrete. I have 50 year old faucet's that are still working perfectly, and 5 year old faucet's that need rebuilt......
I have been looking at building my own honey house. Can you tell? But Mine will have to serve multiple purposes, including the wood shop, so 3000 square feet will not be excessive.
You can ALWAYS use more room, but getting more room isnt as easy as HAVING more room.