From the manual: http://bowtie-bio.sourceforge.net/manual.shtml

Alignments involving one or more ambiguous reference characters (N, -, R, Y, etc.) are considered invalid by Bowtie. This is true only for ambiguous characters in the reference; alignments involving ambiguous characters in the read are legal, subject to the alignment policy. Ambiguous characters in the read mismatch all other characters. Alignments that “fall off” the reference sequence are not considered valid.

So any ambiguous character in the reference overlapping potentials alignment locations will render the read unmapped from what I unerstand.

You can easily explore this by simply making a dummy reference genome, e.g.:

#/ Dummy genomes:
echo ">dummy TAGCTGCGCGCTACGATCGATCGACTGATCAGCGGCTNTAGCTGTACATGCA" | tr " " "\n" > dummy_N.fa
echo ">dummy TAGCTGCGCGCTACGATCGATCGACTGATCAGCGGCTCTAGCTGTACATGCA" | tr " " "\n" > dummy_no_N.fa

#/ Index:
for i in dummy*.fa; do bowtie-build $i $i; done

#/ Dummy read (same as the dummy_N.fa sequence)
echo ">dummy_read TAGCTGCGCGCTACGATCGATCGACTGATCAGCGGCTNTAGCTGTACATGCA" | tr " " "\n" > dummy_read.fa

bowtie -f dummy_N.fa dummy_read.fa
# reads processed: 1
# reads with at least one alignment: 0 (0.00%)
# reads that failed to align: 1 (100.00%)
No alignments

bowtie -f dummy_no_N.fa dummy_read.fa
# reads processed: 1
# reads with at least one alignment: 1 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 1 alignments