That should be possible in Ascii Sector as well, so that's a bug. I'll check it out...
EDIT: I just tested two patrol missions in the same system and using the same nav points. Both had Pirate encounters and the only thing I noticed was that sometimes a misson objective in one of the patrol missions was completed just by passing through the nav point (even though there were still Pirates around), while the other mission's objective wouldn't be completed until I had destroyed the Pirates. This is because each Pirate ship is associated with a mission. When you pass through a nav point, it checks if there are any Pirates associated with the missions relating to that nav point. So, when there are two patrol missions using the same nav point, the Pirate ships will only be associated with one of them. After killing the Pirates, both missions' objective at that nav point were completed, however, so that wasn't a problem.
If what you're experiencing is different, it's probably due to a bug that was probably fixed when I fixed another bug relating to scout and patrol missions (sometimes mission objectives wouldn't be completed, even though you passed through the nav point).