Problem with Naboo vs HDDs is that even though taxation gives cheaper units, the best usual counters against HDDs (HMDs and grenaders) are weak with the Naboo. Naboo do not get the HMD upgrade (though they get some good general mech upgrades that improve them).
So when playing Naboo, Air and Jedi are their strongest units vs HDDs, and even with taxation they are not cheap, and they are not easy to mass. You will need to be flexible - go with what the enemy gives you. Use Air units (bombers are the best vs. HDDs) if the enemy is lacking air defense, use Jedi to convert some HDDs and back up these units with some admittedly weak grenaders or MDs. Put up a shield generator to cover your jedi and other units if possible.
I think that the Naboo have the hardest time with HDDs of any of the civs, because I have found the HMDs to be most effective against those units