Thanks to Community members Fred and Data an issue was brought to the forefront dealing with a massive slowdown issue.
In digging through the issue it was directly tied to the latest patch specifically being the new tooltips to help when ordering crew members to perform a direct order.
Alpha 5.3.2 Patch Notes
CREW MANAGEMENT
- Updated the crew management window for quicker schedule alterations.
PERFORMANCE
- Addressed a performance issue dealing with saving the game and the new tooltips implemented in 5.3