Each conning tower adds drag when the boat is submerged, and several add more drag than one big one. So the short answer is "no", it wouldn't make sense.
However...
Up to about 1945, and certainly in the inter-war period, submarines spent most of their time on the surface. They were torpedo boats (or "cruisers", if we're using Corbett's classifications) that could submerge for short periods in order to evade detection, not ships that were primarily undersea vessels.
So if you can find some large piece of equipment that is useful when surfaced and can't be placed inside the pressure hull, you could get a seperate "conning tower" built to house that and provide a bit of streamlining. The obvious thought is a mount for a large gun (6" or more), or a hangar for an aircraft.
It's also worth noting that the early American missile subs - those carrying Regulus missiles - had large external fairings to contain the missiles and launch gear. Something like that might give you the excuse you need to have something very similar to a second conning tower.