Would cleaning FTC_FleetHistory make a noticeable difference ? What exactly is stored in it ?

To answer your latter question, in-game each and every fleet has a history of the actions it's taken dating back to the initial formation of that fleet. So a cargo fleet might have records of picking up mines on Earth, unloading them on Luna, etc. Deleting the entries in FCT_FleetHistory removes all those records. There's no gameplay effect, but if you RP a lot or want to know what a particular fleet did at a particular time it would remove that information.

Once I found a large freighter that seemed to loop around its orders many multiple times uneccessarily (without throwing an error) and fill up its event log. I detatched it to a new fleet, deleted the old one and it made a huge difference.

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As to your question, that does sound little long for what you describe. However, Steve has put out version 2.1 already so I would recommend to switching to that unless you're really attached to your current game. If you are, then deal with the NPRs as soon as possible since they are the likely culprits of major slowdowns if you've already purged civilian shipping lines. Also, if you have the "NPRs activate spoilers" option toggled on, then your game might be screwed in the sense that the 2 or 3 NPRs could have generated multiple spoilers that are now busy grinding your game down to a crawl.