How can I check if a reference frame is used?

Nothing built into FrameMaker, but here a simple script that you can use. Copy the script and put it in a plain text file with a .jsx extension. Open a FrameMaker document, and choose File > Script > Run and select the script. It will write the paragraph and paragraph format Frame Above and Frame Below data to the Console. You can copy the Console text and import it into a spreadsheet, using the pipe symbol as a delimiter, and then make a report.

Alernatively, you can add the script to the Script Catalog (File > Script > Library) and run it from there.

main ();

function main () {

    var doc;
    
    doc = app.ActiveDoc;
    if (doc.ObjectValid () === 1) {
        processDoc (doc);
    }
}

function processDoc (doc) {

    var pgf, pgfFmt;
    
    Console ("----------");
    Console ("Document paragraphs:")
    pgf = doc.FirstPgfInDoc;
    while (pgf.ObjectValid () === 1) {
        if (pgf.TopSeparator !== "") {
            Console (pgf.Name + "|Frame Above|" + pgf.TopSeparator);
        }
        if (pgf.BottomSeparator !== "") {
            Console (pgf.Name + "|Frame Below|" + pgf.BottomSeparator);
        }
        pgf = pgf.NextPgfInDoc;
    }

    Console ("----------");
    Console ("Document paragraph formats:")
    pgfFmt = doc.FirstPgfFmtInDoc;
    while (pgfFmt.ObjectValid () === 1) {
        if (pgfFmt.TopSeparator !== "") {
            Console (pgfFmt.Name + "|Frame Above|" + pgfFmt.TopSeparator);
        }
        if (pgfFmt.BottomSeparator !== "") {
            Console (pgfFmt.Name + "|Frame Below|" + pgfFmt.BottomSeparator);
        }
        pgfFmt = pgfFmt.NextPgfFmtInDoc;
    }
}