Since at least 21w20a, Marker-true-armor stands don't show bubbles if submerged into water as described below, in case there is a block below it. It doesn't matter if it's a full opaque or transparent block, and not only glass, but also e.g. slabs or a banner works.

As soon as there is a block, Air replenishes immediately back to 300s, even if Air went already into negative values and thus bubble appeared prior.

I don't know if this is WaI, I couldn't find anything in the Wiki's armor stand history, but the as-is status could be a potential workaround.

Note to map/contraption makers: If you need the space below a water-submerged, invisible Marker-true-AS to be a nonobstructive void, a barrier block would of course not be an option, but you can use e.g. a structure void block (or e.g. the newish light block). You'll surely come up with better ideas as well.

I don't know if it's WaI that Marker-false-AS still create bubbles if fully submerged in water as described below, and if the above workaround for Marker-true-AS is sufficient for mapmakers, or if they'd prefer a full fix.

I hope Mojang can ask the mapmaking community for their requirements, and, dependent on that, this bugpost may be closed.
As long as this is not officially decided, I'll continue to update this bugpost.

Leaving the old bugpost text below for history and comprehension purposes.

Armor stands with Marker set to true create bubbles underwater which breaks immersion, as those marker-armor stands are only usable/producible in Creative and valuable mapmaker tools. Armor stands get this behaviour as they are part of EntityLiving. As soon as the armor stand's "eye height" is underneath water, bubbles appear after 300 ticks (15 seconds).

That's why an armor stand with Marker false does not create bubbles, as long as it's solely with its "feet" in water, but not with its "head" or rather at its eye height:

An easy way to solve this without ugly special cases could be to just let canBreatheUnderwater() return true for armor stands.

Summon command:

/summon minecraft:armor_stand ~ ~ ~ {Marker:1b}

Wait for 300 ticks on newly summoned armour stands for bubbles to appear.