Does pumping a septic system disrupt the tank's ecology?
It is recommended that septic tanks be pumped every 3-5 years, having said that it is not always necessary depending on the usage of the tank. You could simply check the sludge level in the tank to see if it requires a pump out. Leaving the tank without checking it is not a good idea as even though it may seem to be working it may be allowing solids/suspended solids to enter the distribution field, which in turn will case it to fail prematurely. 

In regard to your other question yes it does disrupt the ecology of the tank when it is pumped if the whole tank is emptied but this will right itself and if you abstain from using harsh chemicals that drain to the septic this time frame will be reduced.

Pdf on septic care