(This is the right place for feature requests, but it's better to start separate threads for separate issues.)

1) I would be very interested in having another "search field" on the collection side, so it would be way faster to retrieve a (sub)folder (and not only a specific reference as for now).

Collection search is a common request, and you can find some threads on it if you search. Short version: there's not a great place for it (it would make for the third filter field in the UI), we might figure something out at some point, and as an alternative you can click in the collections tree and just start typing a collection name to select it. Press + on the keyboard first to expand all collections and include subcollections.

2) As I am using zotfile, and frequently importing highlighted sections, it would be nice to have a direct and easy overview on references that have notes attached without having to click to expand and see if there's one.

There's a Notes column you can enable to see if an item has a note. You can also click an item and press + to expand all items.

3) I would love to have some options on the search field for references, as for an advanced research with filters (for example "references with/without notes", "years", etc.)

I'm not sure exactly what you mean by this, but you're aware of the Advanced Search window? The main search bar also includes a drop-down that you can change to search parent items only ("Title, Creator, Year") or child items as well ("All Fields & Tags"/"Everything").