Hey, I had a similar experience and these are the things I remember doing; I hope it helps:

1. On one campaign, I had weirdly overlooked how much hypermatter I was collecting versus hyperfuel I was producing, and so when my hyperfuel went into the red I got away with simply adusting the production rate to match the collection rate. I don't think you made that oversight, but I thought it worth stating in case other people as spacey as me read this.

2. When I'm expanding to new systems, I always prioritize systems with hypermatter deposits first. Tech research that increases the yield of orbital mining stations goes a really long way.

3. When picking planets to colonize, I (almost) always prioritize planets with the hypermatter extractor that you mentioned, especially if there are additional special features with it. I check every inhabitable planet within my borders and bordering my empire for their unique features and focus on the ones that have "special core properties" because, when examined further, that almost always refers to hypermatter extraction. If you want to plan further away from your borders and are seeing ?s for unique features and blockers, then use the console command "intel" to peak at it, so long as you prefer that convenience to the lost immersion that comes from surveying every single system while your fleet runs out of gas.

4. By late game you should have at some resources far in excess of what you need, so take advantage of that at the Galactic Market. Whether you need hypermatter or hyperfuel, you can buy both there while selling (probably) excess food.

5. The single most useful thing when you are low on hyperfuel is a piece of technology and its corresponding planetary building: "synthetic hyperfuel refinery". The tech is under engineering (industry) and in case you just want the console command to learn it now, it's "research_technology tech_synthetic_fuel". These synthetic refineries can make fuel using ONLY energy/credits and can be built on every single planet. If you have this tech and use it, you will literally never be short on fuel again.

I hope it helped at all. Good luck.

Just to add to this. I maximize output by building a Refinery District and fill it to full on planets where I can build Hypermatter Extractors. This further increases Hyperfuel from jobs by 5%.

What you can also do if desperate is build the Synthetic Hyperfuel Refinery building on a starbase. Gives you both hypermatter and hyperfuel in exchange for energy. But I suggest this only as a last course of action. Build the synthetic hyperfuel extractor on planets first.

Refinery District + Ecumenopolis. No need to frack for that hyperfuel anymore!

Synthetic hyper fuel refineries are your best friend.

Refinery Districts on Ecumenopoli will give you 5 districts providing the planet with 5 hypermatter extractor jobs, and 15 Hyperfuel refinery jobs, at a base production rate you should get 120 Hyperfuel per turn(Not counting the refinery bonuses), and generally will produce enough Hypermatter to exceed the upkeep for the 15 refinery jobs.

mousing over the resource tells you the sources for it... just in case you missed.