Can I say : "Here are your shoes" ( if we've found the shoes here )? Can 'HERE' be used in this way? And can I say : "Here these are" (just like : "here it is")?
Here is not the subject: it's the ordinary locative moved to the front for emphasis. The subject is your shoes.
Here is/are X is fine, but it doesn't mean quite the same thing as Your shoes are here—it's used primarily when you hand X to the hearer:
Here are your shoes; I found them under the table.
Here's your book; thanks for lending it to me!
And we wouldn't ordinarily say Here these are (unless we had to distinguish these from some other X, "those X"); we use the 'personal' pronoun they, just as in Here it is:
Here they are; I found them under the table.