BigBizkit

Yes, this should be fixed in the latest version of the extension.

The file Vortex downloads is safe and provides the unstripped assemblies needed for Valheim modding. As you said yourself, unfortunately the uploader of the unstripped assemblies on Nexus Mods decided to hide the files as they deemed them no longer needed since Vortex now pulls them from the source you specified.
 
If the unstripped assemblies were hosted on Nexus Mods or GitHub, then we could pull them from there, but I'm afraid atm. no one is hosting them there.

The game being stuck on a black screen after launching it is indicative of outdated mods in your NativePC folder. The game was updated recently so it's likely you have some mods that have not yet been updated, causing that issue.
 
Make sure the NativePC folder in your MHW directory is empty. It sounds like you still have manually installed, outdated mods left over - as Zaldiir suggested.
 
Please note that mods require Stracker's Loader to be installed and - as Stracker points out on the file page - quest mods/monster mods also require the installation of Performance Booster. Both of these can be installed with Vortex just fine, as can most mods that are packaged properly. Again, the black screen is not caused by Vortex not installing mods properly, it's caused by at least one mod being out of date and not suited for the current version of the game.

For anyone else having this issue:
 
You need to go to C:\Users\YourUser\AppData\Roaming\Vortex\plugins and if there is a folder for Bannerlord/Mount and Blade II you need to delete that and restart Vortex.

If you go to Settings > Interface there is an orange button to "Reset suppressed notifications" - that should do it.

I see now, it seems to be an issue with "Better Merchant" as it is not updated for the latest version. There is, however, an updated version linked in the top comment on the Better Merchant mod page:
 
https://www.nexusmods.com/witcher3/mods/599?tab=posts

To answer your question:
 
As far as Vortex can tell the mods have already been deleted or moved outside the staging folder. Applying those changes would not delete the mods (they're already gone/have been moved out side of Vortex's control) but put the staging folder back in sync.

A missing master means that one of your active plugins in your list is dependent on another plugin, but that plugin is not active in your load order i.e. missing.
 
The problem with that is that, due to how Bethesda games work, the game will crash before the main menu appears (when plugins are being loaded) just after the Bethesda logo.
 
In short: yes it does matter.

Sure.
 
They're in AppData/Roaming/Vortex.
 
On Windows 10:
Press the windows key + R.
Type in "%appdata%" and hit enter.
 
The logs are in that folder and named Vortex/Vortex1/Vortex2 etc.

Glad you figured it out. For anyone else: there are two ways to set Vortex to handle downloads on Nexus Mods.
 
A) Go to your dashboard and on the dashlet that says "Let's get you set up" click the tile that says "Handle Nexus Links". Make sure it is set to "yes".

 
B) Go to your "Settings" (on the left, right under "Support"). Click the rider that says "Download". In the top left corner, enable handling of "Mod Manager Download" buttons.
 

 
 
Either works and will make it so Vortex downloads from Nexus Mods.