Odd oversight there. You can go to a planet, scan 5 plants, and you get SP/Merits. If you fly around space and scan 5 anomalies, you get nothing.
Does it really matter though eventually you get to a point that everything that can be maxed is maxed and you have nothing to spend them on. I currenty have 1695 5th order badges of Exploration unused and 43715 Starfleet merits.