Depending on the certification and date of manufacture, the beacon may not meet the criteria for FAR compliant anti-collision lights. As long as its not on the list of required equipment (KOEL).
I would personally placard the strobe switch as "INOP, ref FAR § 91.213 (d)(3)(ii)? DAY/VFR flight only" and note in the aircraft dispatch paperwork/process that the aircraft is restricted to Daytime VFR only.