The one in the screenshot below seems to be blockaded even though I control the whole route - I think.

There are pirates in the wormhole between Hydrus and that "Astrobrands" intersection but I can't attack them until they come out at one end or the other (which they tend not to do) and I don't see why it should block a route all the way out one 'arm'. Is it just because of the pirate base just below - even though they are a jump away from the route itself with my patrolling ships at the junction?

There is an orange fleet on M2-9 maybe they are blockading the trade route. Also the red fleet in top left corner might also be obstructing the trade. Also usually the trade route blockaded notification allows you to center upon the node where it is blockaded.

The two places Salterius pointed out match up with where the trade screen switches from "functional trade route" (the solid lines) to "blocked trade route" (the dashed lines), so those may indeed be the culprits.

Both of those colours are allies, though!

If they are your allies, then this is indeed odd. Do you still have a save of this?