I’ve spent over an hour researching and testing what is the difference between those two japanese bombers. I only found one difference, which is the exhaust system. However after testing the bombers in game, there is no difference in performance, fuel consumption or cooling, so its only a visual difference. But the repair cost of the L variant is higher by 282 sl, crew train cost is higher by 9000 sl and the price of the researched airplane is higher by 29 000sl. So that raises a very obvious question: Why? I even found an old facebook post by WarThunder, where they added it, but there is no other description than that it struggled in its intended purpose. And it was even higher in br by 0.7 points than the IIb variant back then.
Gaijin should either boost the performance of the L variant (if there was any difference in performance) or lower the cost of the L variant to match the IIb. Or maybe just remove the L variant as a researchable aircraft and make it a modification of the Ki-49 IIb, so new players don’t have to research a new aircraft just for them to realize it is just a reskin of the exact same bomber they already have. Also, maybe Gaijin could replace the L variant with Ki-49 III, which got more powerful engines.
Edit: There is still br difference by 0.3 points in arcade battles.
Edit 2: I found some japanese page saying, that there should be 12.7mm machine guns replacing the 7.7mm machine guns in the sides (which is not in the game), I understand that this is not a valid proof, but maybe it could help with further research: Ki-49-IIb/Late - War Thunder Wiki*.