I've come around to trying to get all of the narrative (as much as possible, but this will exclude action) into thought--the non-italicized kind. I still use italics but infrequently, to go deeper and stronger, they add oomph, like punctuation.
Part of the method to make all the narrative (as much as possible) come across as thought is getting rid of words that work against that goal. Part is voice.
1. The clouds looked menacing. John Doe was certain it would rain soon. The language in your example is sub-par to feel like thought.
2. The clouds lay heavy and dark, and John pulled his umbrella out. This would be a rewrite to make the front end showier and punch that show with an action.
The action is actually reaction to the clouds, which makes the first clause something that's going on in John's head--so that seems closer to thought to me. I'd also not use his last name in the narrative, obviously, though I doubt you would either.
If I were to italicize anything in this rainy moment, it would be something else, a more illuminating thought than "It will rain." Maybe This is a new suit. Or, Thank God, the drought's finally ending. Again, I understand you were going for efficiency in your post.
One reason I try to make all of the narrative (as much as possible) feel more like thought, is because then, something that would sound 'too telly' otherwise becomes camouflaged--by association--into looking like thought.
He was so very sad.
That's a telling phrase, but if the much of the narrative comes to feel like thought, that phrase can feel like thought too.
So--my preference is more at the language level than the font-style level. Also trying to find voice in the narrative, so that the narrative can sound (as much as possible) entirely like thought. I only rarely use italics for thought anymore, and always as follows:
Italics: One of the reasons italics is nice is that when writing in 3rd person past tense, italicized thought is conveyed in first person present. Or even second person after a fashion, and both of those are a bit more... eye-catching.
He was dying, (3rd past) vs. I'm dying (1st present).
The shift to present tense first person adds a kick. The italics add a kick. They make the reader take notice. Like exclamation points. So I never use italics unless it shifts the thought into 1st/present. IOW, I would never italicize It would rain, he was certain, but might italicize This is a new suit.
Those are my thoughts.