I just double-checked to be certain, but all the Enterprise items (NX-01 class ship, standard uniforms, T'pol's uniform, mirror universe uniforms) are missing from the C-Store. Were they intentionally removed, or is this a bug?

The NX is still listed under ships but all the uniform options, from every era, are missing.

The uniform options are in the tailor itself.

For some reason, Cryptic doesn't like having more than one place to get things, so you have to go to the tailor to get uniform options.

If I am understanding the OP correctly, he's asking where they are in the C-Store. And I think the answer is that they're now in the Enterprise Era bundle.

The Dev's did mention last Fall that they wanted to get rid of the 'legacy unlocks' tab use... Many of the Packages have been removed from the C-Store, but they can still be purchased directly in-game... Uniforms at the Tailor, Ships at the Shipyard Vendor, etc...

I guess it just comes down to differences between the in-game C-Store and the website C-Store. Which in itself is confusing....