Is there a point in recalibration of scores for variant calling? The most variant calling pipeline GATK include a Base Quality Score Recalibration (BQSR) which requires a list of known variants. Recently, some work has been done for reference-free recalibration of scores as well: Lacer and atlas, which is motivated by making the most for aDNA and low coverage datasets. 

The importance for aDNA is explained in this lecture, but it is not clear to me if / how is important BQSR is for fresh DNA samples with decent (>15x) coverage. Especially when I work with non-model organisms and I can not simply use the standard tools.

How big an impact does recalibration of scores have on variant calling? Is there a rule of thumb for which it is / it is not worth the effort?
I personally don't think BQSR has a huge impact on variant calling, but you don't really need to guess. If you run GATK BQSR, it outputs a table and charts of exactly how much quality scores are adjusted. The adjustment will vary depending on the position in the read and genomic context (previous and following base). In my experience, the difference is a few points at most, but it's certainly noticeable.

GATK recommends BQSR for both genome and exome data, which is normally much higher than 15x.