How serious it is not to disclose full academic history in your grad school application?
I'd leave it alone, or disclose to your department, not the admissions office.

First, You got all your degrees at one university.  Presumably, the school you applied to was sent an official transcript, and that transcript would show all the degrees conferred by that school.  They have the info.

Second, the odd part about your application package is the MS in EE, given that you're applying for a second MS in EE.  Your new department knows this.  They wouldn't even bat an eye at the second BS.  Dual BS's are fairly common, and it wouldn't be a negative in your package.

Lastly, you gave them what they asked for, which was all universities you attended. You followed their instructions to the letter.