Seems like those existing items are not being considered as project files but as misc files when being opened from solution explorer.
This seems to be an expected behavior
Any files in the dialogue box which does not have extension such as
dtsx or config .Selecting these files will automatically place them in
Miscellaneous folder
How to Add a File to the SSIS Project Miscellaneous Folder
If the file exists on disk (physically in the folder) but does not show in the solution then it is likely that the file was checked in, but the modification to the solution was not. And for BatchFiles folder, you just add them in the source control explorer. That's why there are not the in the solution explorer.
Also will the .dtproj file always be hidden?
Seems to be so. I have also reproduced and got the same behavior like this. Sorry, not very familiar with SSIS project. But according to some tutorials in google such as this
Blog : Building your SSIS project in Azure DevOps It not appears, but we also able to build it through Azure DevOps.