Impossible to answer without knowing what your intentions and preferences are but consider this:

Part of the charm of some of the vessels are their collectability, I think. I have a Freelancer MIS not because I think it'll be an effective missile-boat but because they were a limited semi-"failed" experiment according to lore and now only used by some systems militias. It has character.

I have a Phoenix and, while not seeing a purpose for it now is frustrating, I have a feeling that the more people melt theirs for 600is and others, the more rare it will be. Rarity in this context isn't profitable or a leg up in combat or anything, just something fun. A little special something you don't see every day. There's also a good chance that the revamped version coming will address the criticisms it got last time. I'm this close to melting it myself but this is the one thing keeping me from doing it. I think they'll give it character.

Those things become collectible that others don't care about. You can always get everything else in-game (except a named hull for 600i but... how important is that really).