yes it is worth it but in your case something is broken.
my diseases tick for around 1200 damage at a minimum and crit for 2400-3k depending on the situation. having a disease hit for half that damage for EACH disease on EVERY affected target is significant. if BOTH diseases were hitting for 600 damage that would only = 1 contagion disease damage missing out on the other 1200 damage or possibly a crit PER target. that is very significant on more than 2 targets.
apparently your addon to calculate this is either broken, you are bugged, there is a bug on the server or you are just missing something. What i mean is it is not intended to not cause 100% damage. Contagion is supposed to apply the same damage to all targets affected by your diseases equally (given no buffs on the target preventing damage)