I wonder why there are different levels of security and analysis in Star Trek: if the goal is to be as efficient and safe as possible, why not activate the analysis and / or security systems directly to the maximum level? I guess it has something to do with who activates the analysis or security, but it's still a little stupid, isn't it?
Running a "level whatever diagnostic" is going to impact the day-to-day operation of the ship. It might require taking systems offline and activating the backups, or at the very least it will consume computer capacity, which is still a finite resource.
Think of it this way. On a desktop PC, do you want to run the disk defragmentation, an in-depth virus scan, and an operating system upgrade at the same time?
If you look at Star Trek publications like the TNG Technical Manual by Sternbach and Okuda, it mentions that Level 1, 2 or 3 diagnostics involve crewmembers who look at things. Level 4 or 5 are automated.