What a missing script means
A missing script usually means a serialized component reference points to a script that Unity can no longer resolve. The object may still exist and look correct in the editor while failing at runtime.
Why manual checking does not scale
A project with a few prefabs can be checked by hand. Once a project contains hundreds or thousands of assets, opening every prefab is not a reliable QA process.
Scan scenes and prefabs
A useful editor check walks the serialized object hierarchy and identifies components that no longer have a valid script reference. Keep the scan read-only so developers can decide how to repair each result.
Report context
Do not report only a count. Include the asset path and object path so the developer can locate the issue quickly. Grouping results by asset also makes large scans easier to review.
Repair carefully
Automatic removal can be useful in controlled cases, but destructive cleanup should be explicit. A validator and a cleaner can be separate actions so scanning never changes project data unexpectedly.
Add the check to release workflow
Run the scan before a build or before committing a large asset migration. The earlier a missing script is found, the cheaper it is to fix.
Use a dedicated tool
A focused editor utility can make this workflow repeatable. RomaSoft Smart Prefab Cleaner combines missing-script and reference-oriented checks with project cleanup workflows.
Conclusion
The most reliable Unity workflows separate responsibilities, make expensive work predictable and turn repeated checks into repeatable systems. Start with a small implementation, measure the real bottleneck and expand only when the project needs it.