The only workaround I found is to make the 32 bit dbx in OracleDeveloperStudio12.6-linux-x86-bin/developerstudio12.6/lib/dbx/32 unavailable, e.g. rename it
mv OracleDeveloperStudio12.6-linux-x86-bin/developerstudio12.6/lib/dbx/32/dbx OracleDeveloperStudio12.6-linux-x86-bin/developerstudio12.6/lib/dbx/32/dbx.bak
Which is fine with me as I do not intend to debug 32 bit applications anyway. But I'd still like to know whether there's a more convenient option.