Hah I solve my own problem after reading through the POSIX serial communication. Here is the solution for those who are in same boots:
/* Output options -> Auto add CR LF */
toptions.c_oflag &= ~OPOST;
toptions.c_oflag &= ~ONLCR;
When I sent command and did not get data back that suggested for me that the ardu does not get the command so there is a problem with the PC output.
With these flags the CR LF will be appended to sent out commands, don't ask me why is this necessary since my code is sending \n but it is in NetBSD not in Linux.
So it is half solved. Now the question remains why is /dev/dtyU0 not created at boot time just when I replug the stick.