As long as you are already within the Schengen area, you can usually travel to other countries (e.g. between Belgium and Portugal) without any immigration checks. Due to the 'refugee situation', there are currently more or less permanent immigration checkpoints at some internal Schengen borders and higher chances than usual for a random check at other borders. I do not believe that flights between Portugal and Belgium are affected by these 'temporary' measurements. Some airlines (Ryanair) do however check your immigration status also on flights within the Schengen area and will at least refuse to transport you if you are staying illegaly.
When eventually leaving the Schengen area to go home to Taiwan, you will however have to go through immigration exit checkpoints and you must expect that your overstay will be noticed. The penalties for overstaying are defined in national laws or regulations and depend on which country you are exiting from. You may have to face an entry ban for several years.