Sequence allignment with suffix array?
Suffix arrays vs Suffix tree is a problem quite often discussed in bioinformatics classes, but it's not that much used in practice. Most of people use already optimized mappers bowtie2 or bwa-mem.
I would advise you against your intention of mapping the reads using your own implementation of anything. You don't need to reinvent the wheel, just use an existing solution.
By the way, the Ns in the reference are either hard-masked nucleotides (that would be repeats of some sorts) or (more often) simply unknown nucleotides. So there is no way to map your reads there anyway (and the mentioned mappers will handle the Ns for you).