I believe a lot of the design solution was a concern about the corrosive effect of the exhaust on personnel and equipment but this is something I read 30 years ago.
With surface ships it wasn't quite the same problem. Stick a tall enough funnel or funnels amidships, and you can keep most of the smoke off the decks (and crew) most of the time.
Once navies started building carriers, solutions weren't so obvious. Smoke might reduce visibility for firing directors, but it could absolutely obstruct flight operations. And where do you put the funnel, anyway? Carriers require some fancy and intricate trunking for exhaust thanks to the need to keep space free for the hangar and flight decks. The Japanese seem to have tried the most creative solutions - look at the weird things they tried on
Akagi and
Kaga - but I find it instructive that by the 40's, they ended up adopting similar solutions to the USN and RN, as you can see on the
Taiho: put a big island starboard amidships and trunk the funnel through that. (I gather that while their side trunking usually kept smoke off the flight deck, it wasn't always so helpful on the open hangar deck.) Also it helped that no matter how desperate the IJN's fuel oil problem became they never ended up burning peat moss or potatoes or whatever the hell it is that the
Kuznetsov is using these days.
The
Independence-class is interesting because you'll notice that they trunk four funnels on the starboard side, but the
Cleveland class cruisers (which they're converted from) only have two funnels. As I understand it, the original carrier conversion design did not have an island at all; a small island was added late in the process. But the trunking from the power plant was already designed, so running it all through the island wasn't an option. They were in a tearing hurry to get these flattops deployed, since that was the only virtue, besides speed, they possessed - quick availability.