This is normal in CEP2.

A few invisible parts are by design. For example, some robes look wrong when animated unless you use invisible legs and feet (or fix the 2da).

More commonly, if you switch gender, you will often see that the "invisible" models are actually defined for one sex but not the other.

For example, skirts and dresses are often female-only.

Not ideal, but making models for both genders is hard work (compared to duplicating models for all races, which is automated) and might not have occurred to prolific clothing designers like Lisa back in the day. Unlikely to change, for backward compatibility.

For this reason, CEP allows you to give clothing an item property which restricts gender. You can script your OnAcquire event (for companions) and OnEquip event (for players) to enforce this.

CEP3 is an independent fork in the project, but I guess it inherited the same issues.