"The Coming of Vertumnus", by Ian Watson
Featured one of Gardner Dozois' Year's Best anthologies
Correct, the tenth annual edition.
Was I the Jill Donaldson who had written Aesthetic Concupiscence?
Set in near future
Although a year isn't mentioned, the exorbitant prices of London real estate and the technology level are consistent with the time period the story was written (1980s-1990s).
Protagonist sent to ascertain authenticity of newly discovered Arcimboldo paintings, or something along those lines
Close! She is an art critic paid to write an introduction to an art book of "newly discovered" Arcimboldos that are actually modern forgeries meant to discredit a Green movement using legitimate Arcimboldos as advertising.
She is either drugged and the drug drives her insane, or goes insane naturally, or both
Immediately one hand pressed under my nose and another on my jaw, to force my mouth open.
Liquid poured down my throat -- some sweet concoction masking a bitter undertaste. I gagged and spluttered but had no choice except to swallow.
What had I drunk? What had I drunk?
... and it's all downhill for her from there.
She is attacked by men claiming to be protectors the Habsburg name and legacy
'Libels against a certain Holy Roman Emperor, Miss Donaldson. Thus, libels against the Habsburg dynasty... which may yet be the salvation of Europe, and of the world. Very untimely libels.' The gent raised his cane and slashed it to and fro as if decapitating daisies. 'I am sure you will see reason to denounce your fabrications publicly...'
Features a great bit where she interacts directly with one of the paintings' subjects during a hallucination
Until one day the door opened yet again, and golden light bathed my prison chamber.
Vertumnus himself advanced--the fruitful God, his cheeks of ripe apple and peach, head crowned with fruit and grain, his chest a mighty pumpkin. His cherry and blackberry eyes glinted.
He reached for me. Oh to be embraced by him! To be warmed.
He lifted my paralyzed naked body from its dusty niche.
edit: This is the Vertumnus painting referenced: https://en.wikipedia.org/wiki/Vertumnus_%28painting%29