How serious it is not to disclose full academic history in your grad school application? Here is my story.

I was accepted to top-30 world university to MS in Electrical Engineering(EE) progaram. In total I already have 3 degrees: MS in EE (GPA:4.0/4.0), BS in EE(GPA:3.9/4.0), and Bachelor in Economics(GPA:3.8/4.0).

In my application I misunderstood instructions, which wanted me to list "all universities attended". As far as all my degrees were from one single university I though that I was not obliged to enter all of them, because formally I did list "all universities" by mentioning at least one of those degrees. That is why I decided not to enter "irrelevant" Bachelor in Economics degree and entered only BS in EE and MS in EE degrees.

After few months I was successfully accepted to the degree program I had applied to.
But after talking to some other applicants I understood that in application form they wanted me to enter not "all universities" but rather all degree programs attended. So I believe that I should have listed that economics degree as well.

Apparently, concealing this degree didn't give me any benefits during admission, but most likely even might have "downgraded" my application to some extent. So I unintentionally presented myself to be worse that I am in reality.

What do you think I need to do? If I contact admission office I can end up being rejected and I cannot risk that much. 

On the other hand, If I enroll and then they disclose this fact what they most likely will do?
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.