***spoiler***
The Reapers get a specially-bred Breeder queen anyway, presumably via Cerberus (who, we know, were still experimenting with Rachni even after the Noveria experiment was resolved, as completing Noveria unlocks a number of ME1 side-missions involving loose Rachni whether the queen was killed or not).
The effect of saving the Rachni Queen on Noveria is simple: it means that the Queen who the Reapers attempt to use will be indebted to Shepard personally, and will already have set herself against the Reapers prior to ME3. This means that it's possible to rescue her and sway her and her children to the side of the galactic alliances. You can attempt to do this with the Reaper-made Breeder, but by all accounts this attempt will end in disaster.