1) Your files are local
The benefits from this should be pretty obvious: fast access, no waiting for (potentially lengthy) downloads, no worry about incomplete or corrupt downloads, etc.
2) You have the opportunity to handle the lack of network connectivity gracefully
This is a requirement for Apple, BTW. Your app must /at a minimum/ alert the user appropriately. Not displaying a UI or a blank screen or the like is not acceptable.
3) Consistency
All your users on a particular version of native code also have a particular and known version of your web code. It always helps when debugging to eliminate potential issues, and this could be a biggie. What if your user has a corrupted version of your web files? What if a download was incomplete? Good luck debugging that (unless you're also checking the download integrity, and even then, hashes aren't guaranteed to be unique for any given input!)
4) Security
The download from the App store is about as secure as you can get (note: I'm not saying it's /perfectly secure/). If you download the files yourself, you have to worry about the validity and integrity of the files you download. That's not to say that it's impossible, just harder and riskier. The cost of implementation may not prove beneficial wrt the risk of losing your data.
(Oh and don't forget that if someone were to modify your files in transit, now they have access to all the plugins your app has installed. Depending on those plugins, that could be disastrous.)
Finally: Use known and well-tested solutions to do this if you must: don't go building your own solution. Make sure that whatever solution you use can verify that the server it is connected to is the one you expect (SSL certificate pinning / fingerprinting) and that it properly handles incomplete/corrupt file transfers. You should also consider your user's network in this too: an LTE or WIFI connection isn't guaranteed to be fast!