The ship costumes you're referring to, the purely cosmetic ones, have now been folded into the Fleet Ship system, and are only accessible to the Fleet variants of those ships. You can pick up a Fleet ship by joining a Fleet with the appropriate shipyard tier, and exchanging Fleet Marks and Fleet Ship Modules for them.
Long story short, if you want your ship to look like a Nimbus DSSV, Nomad Star Cruiser, Comet RSV, Maelstrom Patrol Escort (formerly the "fleet escort"), or Hephaestus Advanced Escort, you'll have to pick up the Fleet versions of those ships.
That said, if you DID buy the costumes before Season 6 (like I did for the Nimbus, Maelstrom and Comet), you can still use them on any non-Fleet version you own, on any character you own (unlike Fleet ships, which are per-character unlocks). Also, if you bought any of the existing ships off the C-Store that come with new skins, like the Bellerophon LRSV or the Thunderchild Escort, you'll have access to those skins on the Fleet versions of the ships, should you choose to pick them up.
You're referring to the Imperial Class Assault Cruiser, though, and I haven't seen a mention of that skin on this post.
It's possible that Cryptic/PWE intend to bring the skin back whenever they debut a Fleet Assault Cruiser or some kind of refit/retrofit.
Otherwise, you're a few weeks too late I almost regret not buying those skins either, the Nomad and Hephaestus looked cool! On the upside, I can fool people into thinking I have Fleet versions of the DSSV and RSV now.