I have http://skyrim.nexusmods.com/mods/16815

Basically, it does these:

• Duplicate a bunch of vanilla forms
  
• Add a bunch of FormLists that contain vanilla forms (not the duplicates, but actual vanilla records)
  
• Add a few scripts that rely on said FormLists
  
• Add a few quests that uses said scripts
  
• Add a standalone magic effect

What it doesn't do:

• Modify vanilla meshes in any way
  
• Add any new areas
  
• Mess with NavMesh
  
• Tinker with Leveled Lists
  
• Modify any actors

The mod is made with customization in mind, as in, you're going to modify the plugin itself a lot. Currently, the mod is in .esp form, and this proves to be a bit problematic with updates.

Is it safe to esm-ify it? If yes, what is the best way to do that?

I'm asking because I heard there will be problems with NavMesh or some such when you esmify plugins.

Use TESVGecko to convert to master.

Will there be side effects like NavMesh problems or the sort?

You said your mod doesn't do anything with navmesh. Did I misread your enumerated list?