I'm still playing 2.14 (Beyond).

Mostly the fleet Missions in the freighter last 50minutes - 5 hours.
Today the missions last 5 hours - 30 hours.
Is that normal?

I mean i like it, but i wanted to know why they last so much longer now. Is that because i bought a fourth ship for my fleet or if i continue in the main story?

I've had some frigate missions which were quite long, although none longer than 14 hrs-ish (so far).

It's possible that they scale with difficulty

Yes. I have not tracked the full cycle but for at least a year I get a week to ten days with a mission greater than 24 hours mixed in, one day with two missions greater than 24 hours and then about five days or so with all missions less than 24 hours. The long missions also somehow get locked to a randomly selected command room such that if a long mission was in #3 then the next long mission would not be made available until the current long mission was completed although in a couple of days of that long mission cycle locking to a specific room does not occur.

I do not know what the trigger but this pattern started about the same time that frigates upgrading their stats peaked. All frigates stopped having stats increment and all stopped at the same time regardless of where they stood.

EDIT: Should have noted that I have the full complement of 30 S-Class Frigates and try to send out 5 missions at a time. You can build a 6th control room and actually have 6 missions in progress at a time.