Thanks for your question! I don’t know why WD is missing data, but maybe Brian or someone here on the forum can address that (?). WXSIM (through its WXSIMATE module) is set to read data from Weather Display, Cumulus, Virtual Weather Station, and WeatherLink. I haven’t seen loggernet before, but will take a look. I don’t know whether or not it’s OK for you to have both WD and loggernet running, but some missing minutes of data will probably not affect WXSIM, as it can use averages over 10 minutes, for example. I’m sure there will be some solution, but you’re right to figure that out before buying! 
Tom Ehrensperger (WXSIM developer)