Dylan Thomas' poems are full of symbols and images and this often adds to their complexity and ambiguity. You should also keep in mind there is rarely only one coherent interpretation of a given poem, and The Ballad of the Long-Legged Bait is no exception. What I offer here is one interpretation; you should consider other possibilities as well.
The most obvious reading of the poem is that it's about the possibility of salvation via the subsumption of sensual desire. The voyage of the fisherman can be construed as the process of purification. Let's consider some of the imagery in order to see whether or not this interpretation can be supported.
First, we have the fisherman using a girl as bait:
For we saw him throw to the swift flood
A girl alive with his hooks through her lips;
We are also told that "Sin...had a woman's shape". Consider, also, stanza 4:
The sun shipwrecked west on a pearl
And the moon swam out of its hulk.
The sun, here, can be interpreted as a symbol of masculinity and the "pearl" on which it is shipwrecked can be interpreted as a symbol of femininity; the moon, too, is usually a symbol of femininity. The "Funnels and masts" in the following stanza highlight the female/male imagery. The "long-legged bait" is cast into the "sick sea" which is full turmoil and "every beast" and "every turtle" participates in the "Huge weddings in the waves". The death of the girl, however, frees the fisherman from his preoccupations with sensual pleasure ("Mast-high moon-white women naked / Walking in wishes and lovely for shame") and allow him, eventually, to ascend to a higher pleasure.
The symbols — as well as direct references like "Lucifer" — also bring to mind the Bible (especially The Book of Revelations). All these reinforce the theme of the mortification of the flesh and the rewards it brings.
While this is considered a ballad by Dylan Thomas himself, this indicates that there is perhaps a personal story behind the allegory of using bait to catch fish. Perhaps the bait is a long-legged girl that has caught the fisherman. After all, that is what bait is. Bait is used to trick the fish into biting, which ultimately leads to the hooking of the fish. The bait is a trap. The bait is used to take advantage of an unknowing fish.
Perhaps the fisherman was trapped and seduced by a long-legged girl who ultimately caught him. Parallel to the analogy of catching a fish, the fisherman is caught by the bait. He is an unsuspecting victim. He did not realize that the bait was used to trap him. Now, to his sorrow, he is facing the consequences of his actions. He bit the bait, hook, line and sinker. Now he has to live with the fact that he is captured, possibly against his will and he is no longer free to swim the depths of the liberating ocean of life. He has fallen for cupid's arrow through his attachment of the long-legged girl. Dylan Thomas is possibly the fisherman and is speaking from his own personal experiences. He possibly has fallen for the bait of a beautiful long-legged girl. He will never be the same. Once a fish is caught, it is the end of the fish's emotional, mental and even physical former self. There is no way to recover from the wounds of desire. The fisherman has experienced the desire to chomp at the long-legged bait. He will never forget her. He cannot enjoy the freedom of the ocean because he is tied the reel and rod that has taken away his freedom of adventure. He will never return to the innocence of his independence because his heart has tasted the bait of the long-legged girl. He is smitten. He is conquered. The fisherman now sails in darkness and scan only see the light through the violent thunderstorm of lightning.