If anyone else is interested, I e-mailed the author and he said:
"One possible solution is to use the next best alignment score (ZS:i:, previously XS:i:). If the next alignment score is the same as the primary alignment score (AS:i:), that means there are at least two equivalent alignments found by HISAT. This additional SAM field (ZS:i:) is only available at HISAT github, which I’ll include in the next release of HISAT."
The most recent release of hisat (v0.1.6) uses NH tags in the BAM to specify the number of alignments for the read/pair (see release notes: https://ccb.jhu.edu/software/hisat/index.shtml). As far as I understand it, reads/pairs with NH:i:1 have a single best alignment and are therefore "uniquely" mapped.
There is the -k option to inquire a given number of alignments as output. However,since HISAT doesn't finds/reports alignments in a specific order, the -k cutoff won't necessarily give you "best" alignments. So I would not recommend using -k 1 if you want to find the best unique alignment for each read, but it's faster if you want to know whether a reads aligns or not.