Theft generally involves an intent to permanently deprive someone of property, or knowledge that one is taking actions that have the very likely probability of permanently depriving them of property. Here, there is an intent only to hold possession of the keys during the shift and to return them.
Also, while the surrender of keys is contingent upon the incentive of further employment, it is still a voluntary surrender of the keys.
The place where theft issues could arise is if the keys are not returned by the person holding them, either at the end of the shift as punishment, or in mid-shift, if someone insists upon their return, either in an emergency or because they are sick of this manager and want to quit. If keys were retained in those circumstances upon a demand for their return, there might be a problem.
This is because continuing to refuse to surrender possession of property permissively given to someone when that permission is revoked, in the absence of a legal right to impose a possessory lien, would generally constitute theft.
While the purpose for the manager holding keys in this particular situation don't seem very valid, I can imagine circumstances (e.g. MRI technicians, jail guards, underwater divers, the site only has tandem parking), where retaining keys during a shift might be reasonable and appropriate.