RNA_Seq data aligned used uniquely or multi mapped reads impact on result interpretation
There are several methods/tools that take into account multi-mappers and deal with them in reasonable ways (e.g. pseudo-alignment methods like salmon and more traditional alignment-based methods like RSEM). If you completely ignore multi-mappers, then yes, you will be losing information, which may or may not be valuable to you.
Both of those methods utilize the expectation-maximization algorithm (or a variant thereof) to determine the relative contributions of multi-mapping reads to the various mapping locations. With salmon, you can forego alignment completely and end up with very accurate gene quantifications in hand in like 20 minutes if you want.