I don't see any reason why you could not do that.

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84 300D, 82 Volvo 244Gl Diesel

I don't see any reason it would hurt to cap each nipple off. You normally don't want to do that on U.S. engines because I think that will dead-head the water pump when the engine is cold and the T-stat is closed, which could make the blades cavitate, if someone is stupid enough to race a cold engine. But, as mentioned, M-B uses the common Euro design where there is an adjustable bypass which gets closed by the T-stat as it opens the return from the radiator. The T-stat is like an alien w/ 2 block-off disks. U.S. cars usually have a single-plate T-stat and an always-open bypass hose.

The electric "aux water pump" is unneeded. I took it off both my 300D's. It is a place to leak coolant, block heater flow, or cause a dash fire when the motor stalls and draws too much current. My guess its purpose was to move water with the car left idling outside on a cold, dark German winter morning. The heater core is a giant 3 tube Behr design (1 tube in, 2 out or vice-versa), with Rube Golberg plumbing on the firewall to match. You see the same in semi-truck cabins. When you do add a heater, just use a basic 2-tube one, preferably solid copper.

Re hot-water control. In 1960's U.S. cars w/o AC, there was no water valve and it flowed hot water all the time. The cabin blower and mix door (outside air) adjusted cabin temperature manually. AC cars had an on-off hot water valve, usually controlled by vacuum, some a single-hose and spring and others push-pull vacuum hoses. I bought some little plastic valves (1-hose) for a newish Ford for $7 to maybe use in my classic cars. That is because the heater core was often in the same air path as the AC evaporator. I recall my M-B has separate paths and divert door.

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1984 & 1985 CA 300D's
1964 & 65 Mopar's - Valiant, Dart, Newport
1996 & 2002 Chrysler minivans