In defs.ini, all *.log files are excluded from a sync. These are part of, for example, the AEILocalInterp thorn. I don't think that these should be deleted.
SimFactory does not sync complete thorns, it only syncs those parts that are "necessary" or "useful" at the remote site. For example, repository information is not synced. In particular, SimFactory assumes that no code development occurs at the remote site, and thus excludes the potentially large log files that are mostly useful for inspection by humans while debugging.
Of course this can change. Why do you think these log files are useful on the remote machine?
I do not know what these ".log" files are, and I'm not sure that SimFactory should claim to know either. Making up an example, it could be that some thorn requires some lookup table of logarithms which it calls "table.log". I think it is safer for SimFactory to sync entire thorns, with the exception of version control directories which are fairly well-known and standardised.
One solution would be to exclude specific .log files which we know are not required, by giving the full path of the file, e.g.: