I guess the at first sight different meanings of the word "scene" as traditionally used in theater, live action film and animation aren't so different when you remember it refers originally to the theater play's backdrop: what happens on stage in one scenery in temporal sequence requires one scene in front of which it happens, and that's what it's called: a scene. The same thing would possibly be shown not in one but a number of shots of the same set in live action, therefore the sequence of those several shots is still referred to as one scene. For animation, a new scene, namely a new BG, is required for each shot, therefore what you'd call a scene in live action is a called a sequence here, and the single shots are, quite rightly, called scenes.
Only if there's more than one project in the pipeline or if it's a series, you'd rely have to specify project name or episode number also: Ep__Sq__Sc__ (as David described above)
Unlike the editing process of a live action movie, where you figure out the exact order of shots after producing the footage anyway, an animation is usually "edited" before production as a storyboard or animatic, and because of this it's useful to have sequence and scene start not as no. 01 but as no.010. Like that, you can add new sequences and scenes (starting with, say 015, to leave more room either side) during production when you realize you'll need them, but without messing with your established names, being at the same time crystal clear about where in the movie this new sequence or scene has to go.
As far as I encountered it, that was generally the naming convention as long as live action and animation went pretty much their separate ways, and I still find it very useful personally, particularly the zero-figure-zero convention. But suggesting such a system to live action people you want to colaborate with usually puts some sort of expression on their faces... well, try it!
I guess by now it's best to come to an agreement with the almighty editor before you even start storyboarding.
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TvPaint Animation 11.0.6 Pro