This question already has an answer here:
On Windows and OS X, if Mathematica is already running, double clicking a notebook doesn't open a new Front End instance. Instead it will conveniently open the notebook in the already running instance.
How can I achieve the same behaviour on Linux?
from the command line always opens a completely new instance of the Front End on Linux, even if another Front End was already running. I believe graphical file managers simply run this command when double clicking a notebook.