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You can also check the "Loadout" in the Hyperion information, under Equipment section if you already have a docking computer then it will be under the Thrusters, that's where mine is listed, just in case you have one you had not noticed.
Otherwise with the Hyperion selected, right click on a shipyard (its an L ship), use the command "Upgrade / Repair at", then make the upgrade changes you need in the upgrade screen (try and add crew or change other things as well), confirm changes on the right (may need to scroll down) and pay for the changes.
You can either stay on the bridge and see if the upgrades work after the ship undocks or you can either teleport out of sector/fly a small ship out of sector and let the upgrade work, then check its "Loadout" tab once its undocked from the shipyard.
If that still does not work for you then you may have to put in a bug report and send in a copy of your save etc.
Note on weapon upgrades, if you have Modifcations on any weapon then that must be Dismantled FIRST before you can change a weapon, on the Hyperion only turrets should be changed. With the correct research you can add modifications to different parts of the ship, shields, engines, weapons etc.
You will have plenty of time in the Upgrade screen because the Hyperion will not move at all until you have paid for the upgrade task, then the captain should do all the work.
I've sent many collected or damaged ships to a shipyard/warf to get upgrades with no issues in this same way, so fingers crossed that will help you.
Mind it is unusual not to have a docking computer at all, but you can easily fit a Mk 2 and make life much easier to dock.