Is it acceptable to have two circuits with a shared hot but different neutrals?
Generally speaking, no.
In order to do it this way, they probably ran individual(unsheathed) wires, which is against NEC. From this related question, the relevant NEC is

NEC 300.3(B) requires that:

All conductors of the same circuit ... shall be contained within the same raceway, auxiliary gutter, cable tray, cablebus assembly, trench, cable, or cord [with certain exceptions that do not apply here].


The logic here is that you want to minimize the exposure of the wires. Sheathing helps prevent a small nick from turning into a big shock.
If you're going to upgrade this the proper way, you would run, say, a brand new 14-2 to your red fixture, and then from the red fixture to the blue fixture. Thus they would share the same hot and neutral circuits properly
EDIT: Since these are inside conduit, that's considered acceptable.