Confirm it is the mods
Back up your saves, disable every mod, and launch the game. If it starts cleanly, you have a mod problem rather than a game problem — and you should not file a bug report with the developer until you have done this.
Re-enable in halves, not one by one
With a long mod list, turning mods back on one at a time is slow. Enable half, test, then split whichever half fails. Five or six launches will find the culprit in a list of fifty.
MOMI already skips some broken mods for you
MOMI intentionally skips mods that use MMAPI when MMAPI detects that the game’s code has changed in a way that would break them. If a mod silently stops appearing after a patch, that protective behaviour is the likely explanation rather than a failed install.
Check each mod’s page for a version bump
Mod authors usually publish an update within days of a patch. Before troubleshooting further, check whether the mod has a newer file listed for your game version — and check the comments, where compatibility is usually reported before the description is updated.
The engine beta is a special case
The new engine beta branch does not support mods at all, its progress is not merged into the main branch, and saves should be backed up before switching. If you are on the beta branch, mods failing is expected behaviour, not something to debug.
Primary sources
Checked against these public pages. Official sources define confirmed features and status; community sources are labelled as such and used for game data that the developer does not publish directly.