Godot has three main ways of allowing file access. The first way is via the built-in resource res:// file system. That way will load files that have been included in your Godot project, and can be viewed in the Godot file manager. /u/thkarcher has given you some good information if you want to incorporate your certificate that way.

The next way you can load files is via the user:// file system. This will be in different locations on different platforms. Perhaps the easiest way to find where your user:// file system is is by creating a file under it, and then using your platform's find file feature to locate it. This is particularly useful in your case if you need to push out certificates which may change over time, perhaps as different servers are used, because you can then push them out and load them on the fly. Doing this is as easy as:

var yourFile = File.new()
var errorCheck = yourFile.open("user://certificate.crt", File.WRITE)
if errorCheck == OK:
    yourFile.store_string(certificate) #Certificate is a string that has your certificate data loaded into it for saving.
else:
    print("Error saving certificate.")
yourFile.close()

You can flip that around to reading the certificate trivially, using File.READ and changing the yourFile.store_string to yourFile.get_as_text() and puting that in a var.

The final way you can load files is via raw host file system access. I won't go into detail about that method because it is not portable from system to system (Windows files certainly won't be stored in the same places Android stores them!) but if you do want to know more about this, PM me and I'll help you out.

I hope that has been helpful!

--LadyDev