2) I don't understand you about "option to generate them automatically" and what it doing with URLs.
This is "SEF url options":
What I must change here to use everywhere only full canonical URLs, which I have in field "Hikashop -> Products -> (some product) ->
Canonical URL"?
For example, the field have value - /kolekcija-cajeva/
cajevi-list-cejlona/crni-caj-uva-70107.html
but Google indexing address without product category - /kolekcija-cajeva/crni-caj-uva-70107.html
or the field have value - /kolekcija-cajeva/cajevi-kolekcija-knjiga/zeleni-caj-tea-book-volume-3-green-70289.html
but Google indexing some strange address - /kolekcija-cajeva/cid-117.html
P.S. I really don't understand where he's taking this URLs, which I don't have on web site or in site map?