There are all sorts of reasons for that to happen. Number one used to be computer resources, but most modern computers can handle SH4 with two hands tied behind their backs. The use of Time Compression can also cause issues, and if you are shelling out to the Windows desktop to do email or other chores while playing, that can introduce troubles. Also, doing your "Saves" on top of each other, that can also contribute to the issue. Make each Save unique with a new name, and delete old, unneeded Saves - using the game interface...
The Stock game doesn't gain too much advantage by their use, but any modded game will generally benefit from applying either
LAA or the
4Gig Patch - LAA is pointing at a CapnScurvy write-up on its use on his new install of Windows 10, and the links for the download are in his thread. The 4Gig Patch is from NTCore, and has a bit of a write-up also. You do need to have a 64-bit Windows to use those little applets. Another way the issue you describe can happen is by a bunch of traffic in your vicinity, which might be an area of roughly 30-100 square kilometers, or 20-60 square miles. The traffic doesn't have to be seen yet, for it to slow you down. But if you have a minimal computer system, no LAA, and encounter a 24 or more ship convoy or Task Force, that can really impact your computer - especially if there are errors involved.
I mention this, because some older mods have improperly terminated ships, that just keep circling the globe, while others keep spawning, and the "group" of ships near you might be 100 or more DD. This was bad in some older FOTRS versions, but it was not alone in this. If that's what you have (FOTRS - not FotRSU), let us know, and we have a small "patch" somewhere on one of my hard drives in the basement we can post somewhere for you...