The hole you circled is a bolt hole. A case bolt goes in there.
The filter is not really useful for a CB360. We have no Positive Crankcase Ventilation. PCV valves are connected to intake manifolds and draw air through the crankcase using the manifold vacuum. Since the air is going into the intake side of the engine, it needs to be be filtered. Those filters are what are used. However, the 350/360/450 engines only have a breather tube that allows combustion gases and water vapor out of the crankcase. A filter like that would restrict the breathing of the crankcase, and not needed, since we are not using those vapors anywhere else.
I just tore off my lower case, BTW, and had to remove that bolt (circled hole). That is the only bolt on the upper side of the crankcase that holds the lower half on. All the rest come through the bottom case, into the upper.
You do not need to remove the clutch and sprocket on the crankshaft . You can just remove the chain and starter. CrazyPJ makes a nice machined plug to plug the hole where the starter is mounted. (So do some others). Drop CrazyPJ a note and he could give you pricing and lead time (he makes them himself).