After countless (insert time) searching how to handle an mouse click on an Area2d node, I've came up up with something that works just fine and it's very easy to implement.
1- On the Area2d node connect the signals mouseentered() and mouseexited() to the script.
2- Create an "mouse_over" variable and set it to false.
3- On the mouseentered() function set "mouseover" to true.
On the mouseexited() function set "mouseover" to false.
4- Then on the input function only check if mouseover is true, if the event.ispressed and if the buttonindex is the "BUTTON_LEFT". (left button of the mouse in my case, feel free to change it).
5- Be happy.
PS: "castle" is the name of my node. Godot 3 rc2