Reference genome for allele specific expression
As you said, this is a well-known problem for ASE. In Degner et al. 2009, they state that, "Perhaps surprisingly, we found that masking known SNPs does little to eliminate inherent biases in read-mapping."

As such, substituting N bases is not likely to completely solve your issue. Depending on the aligner, these N bases may also negatively affect your ability to map reads.

Of your two suggestions, I believe HISAT2 will be the better approach. There are also more intensive methods you can use such as empirical Bayesian methods or more traditional variant phasing (ex. AlleleSeq).