The metricsdb files are deleted every 10 secs. From your output, the metricsdb files are not empty. One possibility is that the files are deleted when you open the file. Can you copy these files to another location and inspect them?
Also can you try the following commands for executing perftop? Also I would suggest having this dashboard for atleast a minute so that all the graphs start populating the metrics.
./opendistro-perf-top-linux --dashboard ClusterOverview --endpoint localhost:9600
./opendistro-perf-top-linux --dashboard NodeAnalysis --endpoint localhost:9600
Can you also add additional information about the installation used for spinning up the cluster and the type of system?