The submarines vs. merchant shipping is already a very strange thing in World in Flames, so it is a difficult question to answer, for me, as I look at things from a realism point-of-view. Some players will trade in realism for playability; I would rather increase realism as this game already takes a long, long time to play anyway.
In short: CRUISERS WERE NOT ASW PLATFORMS. It's just a playability fudge. The whole ASW system is that way - Allied investments in ASW are given to them free as the war progresses, for example, when they have to elect to build any other force, such as choosing more strategic bombers or more carriers. The weirdness just continues in so many areas when you compare the game mechanics to history and the whole system could use a major re-write. Sure, it kinda works, just don't watch how it works.
I have had some fun games with the Light Cruisers in play, particularly with the German Commerce Raiders, which aren't ready yet in MWiF.
Oil and the Light Cruisers gets to be a headache, counting manually, as now you have counters that need 2/5, 1/5, 1/10, and 1/20 of an oil point. The players quit moving them even when they can afford the oil, just to avoid figuring out the oil.
But ultimately too with the CL on the board, the navies just never get much smaller, and fewer Battleships ever sink, and having so many pieces essentially doing the same thing gets annoying.
I have liked playing with Presence of the Enemy, Light Cruisers, and a proposed optional rule not available in MWiF, Cruiser Damage, where each result against a Cruiser requires adding another identical result. That rule has it's own plus and minus that I can never recall, though I liked how it encouraged the players to use their Battleships, which have more staying power in combat. I like a robust naval game.
But whatever you do, World in Flames at sea is always an odd beast.