Why are there only two unique semi-independent organelles? Why are there no others, symbiogenesis seems like it should be a relatively common thing. So do most organelles just lose all their DNA? Or is it something that occurs fairly rarely?
There are. But they are not that universal. See kappa-particle in Paramecium and Wolbachia in insects. Also, there are different origins of plastids (compare red algae and green algae). Some organisms like Rhopallodia gibba even have plastids of multiple origin.
So do most organelles just lose all their DNA? Or is it something that occurs fairly rarely?
The organelles of endosymbiotic origin lose their genes gradually. The extent and rate of loss is correlated with the number of organelle the cell harbours. The limited transfer window hypothesis speculates a probable mechanism.