I could be wrong about this, but my understanding is that the EVAP system has a one-way valve, and also some kind of solenoid controlled valve, that is intended to control the venting of the gas tank.
It is normal for this system to maintain a slight vacuum in the tank. Enough to hear it when you open the gas cap.
Of course, it should only be a slight vacuum. If the vacuum gets strong enough to effect fueling then you have a problem.
And yes, removing all the EVAP stuff probably does eliminate the slight vacuum, since now the tank just vents directly to the atmosphere and not under the control of a one-way valve or solenoid. But I don’t think that proves the slight vacuum was itself a “problem.”