I suspect the reason for a lack of end plates on the MS80 was that the tea-tray rear wing was cobbled together quickly when they banned the high wings after the Spanish GP.
At the International Trophy, Silverstone March 30th 1969, the McLarens and Matras had end plates on their high wings. The rest, including Ferrari did not!
By the time of the Dutch Grand Prix, Zandvoort June 21st 1969, the high wings had been banned and the McLarens had end plates as did the Lotus 63 4-w-d. None of the others did.
Finally by the time the teams were at Silverstone for the British Grand Prix in July there were only two teams without end plates on the tea tray wings - BRM and the MS84 used by Beltoise (the MS80s did have end plates!).
Throughout the remainder of the year teams played around with aerodynamics, at some meetings running end plates at others not. It wasn't until much later when the desiners started to utilise aerodynamics to squeeze more speed out of the cars that it became more of a science than a suck-it-and-see approach.