There are numerous issues with your script, you might want to spend some time checking out some of these tutorials brush some more syntax and formatting that will fix some of the problems.

I reformatted it to look a little better & should be closer to running (I can't test it myself);

#!/bin/bash

# iterating over all .fastq.gz files
for fq1 in *.fastq.gz; do
    # create fastq 2 filename by subsituting "_R1_" in the filename for "_R2_"
    fq2="${fq1/_R1_/_R2_}"

    # create an output file name by taking the basename of the input fastq file ??
    out="$(basename ${fq1}_L001_R1_001.fastq.gz)"

    # you are probably going to need to specify the output directory as well,
    # gonna assume its the same as the input directory?
    # give it a new file extension? '.demult.fastq.gz' or something like that
    output_path="$(dirname ${fq1}_L001_R1_001.fastq.gz)/${out}.demult.fastq.gz"
    echo "$fq1, $fq2, $out"

    # you are checking to make sure that both fastq1 and fastq2 exist...
    if [ ! -f "$fq1" ]; then
        echo "WRONG"
        break
    fi
    if [ ! -f "$fq2" ]; then
        echo "WRONG"
        break
    fi

    # I am not really sure what you meant by '${fq1%%.fastq.gz}_%.fa.gz' ...
    fastq-multx -B barcode.txt "$fq1" "$fq2" -o "$output_path"
done

However, there are still a lot of other issues with this script; since I love writing bash scripts, I reformatted the whole thing in a way which might work better:

#!/bin/bash

fastq_dir="$1"
output_dir="$2"
barcode_file="barcode.txt"
mkdir -p "$output_dir"

# find the R1 fastq files, e.g. 'fastq/sample1_L001_R1_001.fastq.gz'
find "$fastq_dir" -type f -name "*.fastq.gz" -name "*_R1_*" -print0 | while read -d $'\0' fastqR1; do
    fastqR1_base="$(basename "$fastqR1")" # sample1_L001_R1_001.fastq.gz

    # split the basename on the last '_R1_' and insert '_R2_'
    fastqR2_base="${fastqR1_base%_R1_*}_R2_${fastqR1_base##*_R1_}" # sample1_L001_R2_001.fastq.gz

    # make full path to the expected R2 fastq file
    fastqR2="$(dirname "$fastqR1")/${fastqR2_base}"

    # make path to output file
    output_base="${fastqR1_base%_R1_*}_${fastqR1_base##*_R1_}" # sample1_L001_001.fastq.gz
    output_path="${output_dir}/${output_base}"

    # make sure fastqR2 exists
    if [ -f "$fastqR2" ] ; then
        echo "Demultiplexing $fastqR1 and $fastqR2 with barcode file $barcode_file, output will be: $output_path"
        fastq-multx -B "$barcode_file" "$fastqR1" "$fastqR2" -o "$output_path"
    fi

done

Usage:

$ ls -1 fastq/
sample1_L001_R1_001.fastq.gz
sample1_L001_R2_001.fastq.gz
sample2_L001_R1_001.fastq.gz
sample2_L001_R2_001.fastq.gz
sample3_L001_R1_001.fastq.gz

$ ./demult2.sh fastq/ output
Demultiplexing fastq//sample1_L001_R1_001.fastq.gz and fastq/sample1_L001_R2_001.fastq.gz with barcode file barcode.txt, output will be: output/sample1_L001_001.fastq.gz
Demultiplexing fastq//sample2_L001_R1_001.fastq.gz and fastq/sample2_L001_R2_001.fastq.gz with barcode file barcode.txt, output will be: output/sample2_L001_001.fastq.gz

Hope that helps.