Fading won't work properly without dmix/resampling on Linux, that's why the option are disabled when ALSA is used and a device is selected. Because when fading, 2 tracks will be played at the same time and that's not possible without resampling. If you select ALSA but automatic for device or use pulseaudio fading will work since then the audio is resampled to 48k.
I have never tested with an iPod Touch. But there are issues related to the library imobiledevice that is used by Strawberry.
You can try to start strawberry from the terminal and see if there are any output.
Also running strawberry as snap has restrictions, you have to connect the correct plugs/slots.
There is an option in the organize dialog to delete or keep original files. Did you select delete original files?
Doing a full rescan should normally fix this if there were just duplicates in the DB that are not actually on disk, but you can check it with the following queries in Tools / Console:
Check if there are songs with identical URL in the DB:
select url, title, album, artist, count(*) from songs group by url having count(*) > 1 order by count(*) desc;
Check if there are songs with the same artist, album and title in the DB:
select title, album, artist, count(*) from songs group by title, album, artist having count(*) > 1 order by count(*) desc;
Deleting all the collection directories and readding will delete everything from songs table so if they still appear even when doing that they are probably duplicates on disk.
We don't really have that. But you can select all songs in the playlist with CTRL + A, then right click and select queue, it will show a number in blue on the right side of the song title. However this will go away when the song is played.