That sounds suspicious on many levels.
For one thing, they already should know exactly how much equity each employee has.
If they don't have those kinds of records, then they're probably going to have a hard time passing a due diligence review by a potential acquirer.
Furthermore, in 42 states, the board of directors can issue equity shares with a simple amendment to the the company's Operating Agreement.
Finally, if the company was operating in one of the 8 states where that's not allowed, or decided to do certificates anyway, the recipients of that equity should not have had the certificates in their hands for long (i.e., they get issued, the recipient has to sign and return within a few days).
So the idea that the certs are floating around out there and must be returned immediately for an acquisition is suspicious.
When the shares are needed, if even one of those people are missing and cannot be found, it adds a pain factor to the process. The physical shares need to be consolidated and accounted for at some point in time. Not everyone leads a stable life where they can be located at all times.
For the employee to physically hold the actual physical share in his or her hand is of no greater benefit than holding a photocopy of the shares along with the vesting agreement and any canceled checks used to pay for the shares. Physical shares can be forged just as easily as a photocopy if it were to go before a judge. It is like having 1 dozen green apples, vs. 1 dozen red apples in your hand. The difference being it is a lot safer for everyone to keep all of the shares in one place.