I see that an old installing procedure for Linux was removed from the site and now there is only an AppImage version.
Could anyone provide me with a good-quality and transparent .png icon for Joplin with square format, without "Joplin" word after icon and white background? It is strange but I didn't find it in my Google search.
The AppImage installation script has not gone. It is still the preferred method as it automatically sets up the .desktop file and the application icon.
When the main site was updated it started automatically offering the AppImage to Linux users rather than the install script. This has been discussed on the forum.
If the suggested automatic download is cancelled and the "full installation details" link on the download page is followed, you go to the general installation page which still shows the script.
If you ever do need a Joplin icon, Joplin's GitHub page is probably the best place to go. 
Yes, I think the main reason I have this question is my low technical experience with a Linux environment. Thanks for all the pieces of advice! Can you please provide me with a script to update Joplin next time? I do not know how to update AppImages... Should I just replace the AppImage file, or it is something more than that?
Use the same script. It's an install AND an update script (Joplin_install_and_update.sh).
But actually my app now located in the folder on my choice. Will the script located it? Possibly it won't.
No it won't.
To upgrade, just download the new AppImage, stop Joplin, replace the AppImage that is in the folder of your choice with the new one, start Joplin again using the launcher you have created. As long as the path or AppImage name does not change all should be fine.
EDIT:
Just re-read your earlier post ...
Yes
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