If it's an illness that he doesn't want to talk about, and which is sapping his strength even some considerable time after he has recovered, then it sounds very much like Covid. I can imagine that if he caught it, given his well-publicised lack of vaccination and all the chaos around his deportation from Australia, then he would be extremely reluctant to admit he'd caught it. IIRC he did catch Covid quite early on in the pandemic, but of course there is nothing to stop someone catching it twice, especially with the later variants.
The problems earlier in his career that sapped his energy were dietary, weren't they? I think it was the switch to a highly-restrictive and gluten-free diet that transformed him from being a good player into a world-beating superman. I don't think his current issues could relate to that.
Of course the problem could be simply that after all his time off, he's a bit rusty and not fully match-fit... and just doesn't want to admit it.
It seems to me that Djokovic is just making excuses. Everybody would have expected that he would have won but he lost and as you mention, he doesn't has played a lot of matches so he is missing some match rhythm.
He is indeed gluten intolerant but already made the switch to the diet a long time ago.