There will not be any operational problems such as crashes or errors when
running a HDFS balancer on a cluster with HBase running, but there can
potentially be a performance impact depending on what the balancer decides
to move based on its space thresholds.
The performance impact would come from loss of locality - the
RegionServers' required HFiles may find their blocks to be remote, so a
slightly higher network usage can be observed until the next major
compaction rewrites a block replica locally.
If you'd like to narrow down the time-frame of impact, you can run the HDFS
balancer with the desired balancing threshold, and then once it is
complete, immediately follow up with a major compaction command on your
latency-sensitive HBase tables.