I didn't get in on the Beta, and I'm not going to be able to play until my copy of the game arrives from Amazon (or Gamestop, whichever comes first) but I've been checking out the ship customization videos on Youtube and comparing them to Suricata's STO Ship Tier Chart, it seems like the customization is essentially swapping out parts from the ships of the type and tier you're in.

For example, it seems that customizing the Miranda class consists of swapping out Saucers, pylons, and nacelles from the Miranda, Centaur, and Shikahr classes, which gives a total of 27 possible hull designs for each tier and type, with other purely cosmetic options (paint scheme) available as well.

Is this the limit of hull customization? Or does swapping out parts (such as deflector dish's) alter the design of your hull as well?

It's not just Saucers, pylons, and nacelles. hulls and struts as well.