The only science consoles I've found so far all seem to buff either astrometrics, photonic theory or spatial anomaly. All three of those are admiral level skills.

Do I get any benefit from those skills as a Lt. Cmdr? I don't see any abilities my BOs have that use those skills, so the consoles seem pretty pointless to me at my level.

Am I missing something?

Yes, you get benefits from them.

My Lt BO with Charged Particle Burst benefits from Astrometrics consoles.

I think so. Admiral level skills buff that particular specific element, that doesn't mean that you can't use weapons/components that benefit from that element from tier 1.

See it like this. An admiral skill could be 'blue photon torpedoes'. You could find MK1 blue photon torpedoes and equip them at level 1 in your Miranda, and a science console that buffs 'blue photon torpedoes' will benefit you even at level 1.

In addition to what Zorac said, Photonic Theory bonuses will improve Photonic Officer and Spatial Anomaly will improve Tyken's Rift, both of which are Lt. Science Boff abilities.