I have a problem similar, that the sim stops for quite a few seconds, even near a minute sometimes. It seems to happen when there is a lot of activity on the hard drive. I have a SSD drive that X-Plane 11 and my /home/username (linux) is on, but the swap partition (for windows swap file) is on a SATA disc drive. I hibernate the computer partway through a flight then resume the next day. This seems to leave a lot of X-Planes open files on the swap partition, that don't get transfered to the RAM memory, even though there is plenty of space left. Or maybe the interuptions are caused by transfer of large amounts of data from the swap partition to the RAM. I know that is the case soon after resuming because it is more often and longer but gets less after time.
Is this anyway related to your aircraft or sim stopping? Maybe not because of resuming from hibernate but could be other applications open in the background taking up a lot of RAM, therefore your computer needing to use swap file or partition. If it is windows it could be a combination of malware continuously hogging resources as it always does, and a fragmented hard drive.