By RAW - yes, but it depends on the form of imprisonment
Firstly, rules-as-written describe the spell Imprisonment fundamentally as a restraint, not something that grants immunity to damage or death:
You create a magical restraint to hold a creature that you can see within range.
Given the context of the forms of imprisonment (burial, chaining, hedge prison, etc.) it's clear that the purpose of removing the requirement to eat, breathe and age is to keep the prisoner alive in the context of the prison itself. This doesn't necessarily mean the prisoner can't be harmed by other means. (Just like a "regular" prisoner, who is sustained by the infrastructure of the prison, can still be beaten up or killed by the wardens or fellow inmates).
Form of Imprisonment
That being said, the ability to actually access the prisoner in order to do them harm depends heavily on which form of the Imprisonment spell you choose to use:
Slumber and Chaining keep the prisoner easily accessible, and within the reach of a convenient beating/smackdown. These are essentially souped up versions of Sleep and Hold Person.
Burial, Hedged Prison and Minimus Containment specify quite explicitly that it is near-impossible to physically access the prisoner (perhaps not without a Wish spell and some generous DM-ruling).