This answer is pretty much a frame challenge.
Your basing the lift for your plants off of vacuum balloons & they don't work because any material strong enough not to be crushed by the air pressure is too heavy to make an envelope from that won't counter all the lift from the vacuum within.
A material with the properties needed to make it work is the holy grail for this sort of thing & it just doesn't exist in nature.
So unless your relying on magic or have large quantities of handwavium in your world you'll have to accept the use of lighter than air gases instead.
If you do try to drop this into a story without magic to back it up I'd predict it will be soundly mocked.
Where you go from there depends on what was important to you, the vacuum balloon nanotubes or the floating islands?
If it's the nanotubes as vacuum balloons then you're at a dead end, the materials to make them pretty much belong in the same category as perpetual motion machines & mechanical antigravity from interrupted centripetal motion, but if it's floating islands you were really after then see below.
Hydrogen is the obvious gas of choice for this.
Easily made from water & plenty of bacteria produce it as a waste product.
It's flammability is going to be an issue but there's really no other choice, it's the only gas with adequate lift to make this even marginally plausible.
Its nearest competitor (helium) is a limited resource that can't be produced by any chemical or organic process.
So we might imagine something like a water hyacinth that produces hydrogen in its buoyancy nodules itself or has formed a partnership with a bacteria that does it for it.
Sargassum is another potential candidate.
You may want the sort of grasping tendrils peas use to help explain them clumping up into great mats to form your islands.
And you're definitely going to need aerial roots such as those found on moth orchids if you want them to remain alive after they've floated off into the air.
The buoyancy nodules will need to be massively bigger than an any existing plants & even then it might be an idea to jiggle with your worlds gravity & air density to make it all a bit more plausible.
I can't think of a single plant with all the characteristics you'd want so basically I'd say just pick one then hybridize & selectively breed it from there, or explain it with subsequent evolution if you want.
I like the water hyacinth so I'd use that, it's pretty.