The presence of a pirate base may cause an explorer to avoid a system. I don't know. Pirates also love to hang around at independents, making them poor refueling sources. The AI knows how to flag "unsafe" systems as seen in the expansion screen on colonies, it could very well avoid them when it comes to refueling non combatants (or even combat ships). I am sure that would be a good idea in general, or you would see frequent situations with out of fuel explorers bouncing in and out of systems like that.
Also, ships gets an order and carries it out. If stopping and ordering again solves something, the situation has somehow changed. Also, how much fuel does an explorer spend exploring a system? The AI could have a somewhat annoying override to reserve a certain amount of fuel, much like Ryan Air don't ;-)
As for fuel, look at this image:
This is the NE corner of a 10x10 ring galaxy, and it is all mine apart for the gas clouds where pirates roam.
You can see my red circled pirate buster fleet near the top heading to kill a red circled pirate base. And there is another one waiting in line. It is based on that yellow circled star base nearby. That one is custom built with a long range scanner and some extra gas extractors. Built because my ships took too long and used too much fuel getting out there, and the pirate bases appeared non stop. The Star Base has 42K caslon, 10.5K reserved (not by that Pirate Buster fleet).
You can see the two other yellow circles. They are former pirate bases kept around as fuel sources. Both have about 13k caslon, all of it reserved. Also the rest of their contents are reserved. So they would not work as refueling points.
This is maybe a hint of too few fuel bases being around. Not that there is a distinct lack of gas mines in that general area. These are not remote areas as seen by the size of the influence circles, so it is a bit different than your shot. But if the bases are busy providing fuel, the colonies have good amounts.
Btw, those repopping pirates are a major annoyance, it is hard to catch them before the ships leave the base. Of course, placing a mine in every cloud with a fuel source would stop them, but...