How to extract only values greater than a threshold

The standard trick for this kind of problem in Awk is to use an associative counter array:

awk '{ print $0 "\t" ++count[$1] }'

This counts the number of times the first word in each line has been seen. It's not quite what you're asking for, since

Apple_1   1      300
Apple_2   1      500
Apple_1   500    1500

would produce

Apple_1   1      300     1
Apple_2   1      500     1
Apple_1   500    1500    2

(the count for Apple_1 isn't reset when we see Apple_2), but if the input is sorted you'll be OK.

Otherwise you'd need to track a counter and last-seen key:

awk '{ if (word == $1) { counter++ } else { counter = 1; word = $1 }; print $0 "\t" counter }'

Read fileB.txt first, make the 1st field a key and the 2nd field its value in an array, skipping the header line with FNR>1 (What are NR and FNR and what does "NR==FNR" imply?).

Then read fileA.txt, print its header for the first line and then print its 1st field followed by the corresponding element in the array, if any.

awk '
    FNR==NR && FNR>1{a[$1]=$2}
    NR!=FNR{
        if(FNR>1){print $1,a[$1]}
        else{print "id", "freq.var"}
    }
' OFS="\t" fileB.txt fileA.txt

OFS="\t" sets the output field separator to tab. Since your file is tab delimited, I assume the output file should be tab delimited too.

You can pipe that into column -t for alignment.