Problem fixed. The problem were the missing parenthesis. Here is the correct query:
http://dsp_url/api/v2/service/_table/tablename?filter=(field1%3D'value1')%20AND%20(field2%3D'value2')
The clue came from here: Service Type list missing after update to 2.04/ admin 2.06
Considering the need for parenthesis were added on 2.0.4, I got one intriguing question on top of my head: instance B were installed using an AWS Bitnami image, already running 2.0.4. Intance A (were the query worked without parenthesis) were updated from 2.0.3 to 2.0.4 a while ago. Could this be some problem during the upgrade process that made this instance run the query without parenthesis even though it was running DF 2.0.4?