I have thoroughly covered "Blue Submarine No. 6" in individual reviews of the four volumes that make up the OAV series.
To avoid repetition, I'll focus my discussion on the differences between the four volume series and the Toonami movie version.
Regardless of whatever cuts Cartoon Network executives made to make "Blue Submarine" more palatable to a wider demographic, it's laudable that the network decided to broadcast this film in the first place. The series grapples with weighty themes, and balances its ultimate argument well by casting humanity in a bellicose light while ennobling the maniacal Zorndyke.
And everything I articulated in the four reviews I wrote holds true. Overall, Cartoon Network's edits primarily include trimming long battle sequences and incidental character lines. The most obvious excision occurs near the beginning of the piece when Mutio, gagging on Oxygen, thrashes about sans nipples. In the original, Maeda's team had been relatively tasteful, depicting the merwoman's breast ends with inoffensive pink dots, something that heightened her air of fragility and vulnerability. Cartoon Network censors simple remove the pink. Not an all-together disastrous call if it came down to a question of whether or not they could air "Blue Sub" or not. But the scene suffers because of it.
Also, as Kino visits Hayami, charged with persuading the old mariner to re-join Blue Fleet, she shuffles through his junk strewn apartment. The Cartoon Network has found it more agreeable to snip those frames in which hypodermic needles and alcohol containers appear. Granted, Hayami's substance abuse problem never factors into the rest of the narrative, but it does add to the sense of hopelessness that has driven him away from humanity.
Slightly sanitized, the Toonami release tells just as powerful a tale as the four DVDs that constitute the uncut story, and runs nearly as long (each of the DVDs only contains one episode).