Well,
Evernote uses a proprietary file format and when you save your Evernote notebooks out to a file the notes have HTML code in them. This you have seen. Joplin will import those files and attempt to save them as HTML which creates all those codes. When you import via markdown it creates a much simpler file format that you're looking for.
It's been a while since I've done an Evernote import but my recollection is that you can import The Notebook as either HTML or markdown.
Do you recall which one you used when you did the import?
If you chose HTML the quickest/easiest way I can think of would be to reimport those notebooks and make sure you choose to import them to markdown format.
I also have some more specific information for you regarding the process of switching from Evernote to Joplin smoothly. I know to convert the proper way to export from Evernote which for some will be tedious what is the only way to recreate The Notebook structure.
I have some information about notes with internal bidirectional links.
There's a bunch of things to look out for and some procedures best followed.
I'm kind of a slug. I am in the middle of a new year of Evernote licensing and I am a subscriber to Joplin cloud at the same time.
I've been learning about all of the ins and outs of moving away from evernote.
GitHub hosts a very nice Evernote export/backup tool that grabs all of your notebooks for you and gives you the ability to save each notebook out as a separate file. This is the only way to recreate the folder structure of notebooks when you import them into Joplin.
Other tips too. For example, I used to use and rely on the Evernote markup feature where you could draw lines and boxes and add text.
I have replaced that with a couple of nice open source tools that specialize in that. One of them is multi-platform so I know it runs on Windows and Linux I'm not sure about Mac.
The other is Windows only but is capable of doing scrolling web page captures among other types of captures and has very good OCR.
You can also set it up to automatically upload a screen grab to your preferred cloud provider and get from the cloud provider the shareable link so you can put it in a note.
Anyway, I will after getting some sleep and then drinking some coffee post my notes so you can look at them and see if there's anything that applies to your scenario.