QNX has no concept of a catch-all console device as you may be used to from other Unixes. There is a console device, yet this handles the text-only BIOS console you find on x86 architectures. The link that you created during startup is not redirecting console output to the serial port as there is no console to start from.
The standard channels used by a process (stdin, stdout, stderr) are determined at the start of the process. In the buildfile the set of standard channels is determined with the 'reopen' directive. So if you use 'reopen /dev/ser1' in your buildfile, this makes all processes started after that directive use the serial port for in and output. If you enabled kernel or startup debugging, then the output will show on the interface even without a serial driver being started, but that is due to the kprintf() functions 'writing' directly onto the serial registers.
If you want to use the serial port differently after the start, you would only need to make sure that all processes that were redirected to /dev/ser1 will no longer print messages, which usually should be the standard case after all. On the other hand it's unusual to share a serial port for (debugging) output and peripherals. If this is a demand by design you may want to look into tty's.
NOTE:
This entry has been validated against the SDP version listed above. Use
caution when considering this advice for any other SDP version. For
supported releases, please reach out to QNX Technical Support if you have any questions/concerns.