Are you asking if gluing the side covers of the hubmotor to the magnet rotor/spoke flange of the hubmotor will block heat transfer from the magnet rotor/spoke flange to the covers?
If so, then yes, in that anything that is between the metal surfaces will add a thermal insulation barrier (even heatsink paste), to a degree dependent on the thickness of the substance and the thermal conductivity of the substance.
(BTW, generally "rim" when discussing hubmotors is assumed to mean the wheel rim, where the tire bead seat will go, and the spokes (if any); some rims directly mount to the hubmotor flange, and so make it even harder to distinguish questions about the actual rim from questions about the "rims" or edges of the rotor portion of the motor, covers, etc. )
What are you using the silicone for?
If you are sealing against water intrusion, it doesn't necessarily work in a typical hubmotor, because both the bearings (and/or the contact surface of bearing to hub side cover and hub axle) and the wiring itself (both where wiring goes thru axle, and inside the actual cable between the wires) can still let in water, at least as humidity in air, as the motor heats up and it pushes air out, then cools off and sucks air back in...usually tiny amounts, but it still happens. In severe wet conditions it can be larger amounts. Then if it's sealed up completely there is nowhere for the water to go. See Justin_LE's video(s) here on ES and on the Grin Tech blog pages or Youtube channel, about water in motors for demonstrations of this issue.
If you have really good water-sealed bearings, and perfect sealing/mating of bearings to axle and hub covers, and truly waterproof connector and shell and contacts on the motor wiring, and truly waterproof seal on the axle wiring entrance, *then* it might work to also seal up the side cover mating surfaces.