It depends on the design and construction of the amp chassis (and the dust cover and base of the turntable). I imagine some amps are put together in such a way that their lid provides structural integrity to the complete chassis, the lid reinforcing the faceplate and rear and side panels by being screwed to them, thereby lessening chassis panel vibrations and the resulting resonances. A better tact is to build an amp without an enclosure containing loose panels to begin with, the way amps were made in the 1950’s and 60’s. Contemporary amps so built are those by EAR-Yoshino, Music Reference, McIntosh, Jadis, Air Tight, Primaluna, Lamm, Allnic, Conrad Johnson, and others. These are all tube amps, which are more commonly available as "open chassis" designs than are solid state ones.
Turntables with a solid plinth, almost(?) universally of non-suspended subchassis design, can be used with a dust cover in place without a sonic penalty IF one does what I have. I have a base that surrounds my table’s solid plinth on all four sides, but without a bottom panel that the plinth sits on. The base surrounds the plinth, but the two are connected only in that they both sit on the same surface, the shelf of a stand. In my case, that "shelf" is actually a Townshend Audio Seismic Sink, whose top plate is relatively dead/non-resonant (the bottom of it’s top panel is damped). Attached to the four-sided base via hinges is a dust cover, which I close after placing an LP on the table’s platter. The resonance of the dust cover is free to migrate down into the base, but is not transferred into the table's plinth, which is isolated from both the Seismic Sink and the base & dust cover by being placed on three roller bearings. True, the air "trapped" inside the dust cover may create a minor cavity resonance, but that is a price I am willing to pay to prevent dust from falling on my precious LP’s during play, far more important to me than any possible slight loss in sound quality!