Thanks @falahfakhri, I’ll try that.
I also tried fixing the SRTM download URL in the snap.auxdata.properties (as in SRTM not downloading) like sed -i 's|http://srtm.csi.cgiar.org/SRT-ZIP/SRTM_V41/SRTM_Data_GeoTiff/|http://srtm.csi.cgiar.org/wp-content/uploads/files/srtm_5x5/TIFF/|g' /usr/local/snap/etc/snap.auxdata.properties and the WARNING went away.
Furthermore, I tried pre-downloading the SRTM tiles in question and placing them in ~/.snap/auxdata/dem/SRTM 3Sec (still zipped), but they still get downloaded every time.
Why is the DEM even used? The setting seems to be only related to subtractTopographicPhase, which is not activated.