SOLUTION FOUND! Thanks to the link suggested by onit here. See the code below: for superuser shell commands to work properly, you first need to create a superuser shell and assign it to a process, then write and read on it's input and output streams respectively.
Process p = Runtime.getRuntime().exec(new String[]{"su", "-c", "system/bin/sh"});
DataOutputStream stdin = new DataOutputStream(p.getOutputStream());
//from here all commands are executed with su permissions
stdin.writeBytes("ls /data\n"); // \n executes the command
InputStream stdout = p.getInputStream();
byte[] buffer = new byte[BUFF_LEN];
int read;
String out = new String();
//read method will wait forever if there is nothing in the stream
//so we need to read it in another way than while((read=stdout.read(buffer))>0)
while(true){
read = stdout.read(buffer);
out += new String(buffer, 0, read);
if(read<BUFF_LEN){
//we have read everything
break;
}
}
//do something with the output