While taking head shots, is it possible to make a not so good looking person look more appealing in pictures?
"Appealing" in what way? What is the purpose of the headshots? – Appeal depends on purpose.
Some people have poor teeth alignment...
You're not going to do much about teeth without visits to the dentist. But it's possible subjects don't mind their teeth. "Poor teeth alignment" is considered attractive in some cultures.
Otherwise, you can suggest expressions with mouth closed.
... some have wrinkles, unpleasant birthmarks or scars due to some accident...
These features can be reduced with soft light and soft focus lenses. However, they can also be points of interest in photos. It depends on the purpose of the photos.
... they simply have poor facial features.
What defines "poor facial features"?
Try different angles, expressions, and distances (focal lengths) until you find something that works.
Try having a short, pleasant conversation with them. Get them talking about a topic they enjoy. Genuine expressions of happiness tend to be considered more attractive.
Many transitional expressions, such as mouth shapes when pronouncing certain syllables, look strange because our brains normally filter them out. (Similar to white balance issues.)
Disfigurement, such as in people who require prosthetic facial pieces, is a more difficult issue because of the risk of turning the subject into a spectacle. If the photo is commissioned by someone other than the subject, consider refusing to take any photos unless you are sure the subject agrees and is fully aware of how the photos will be used.
If the subject is the client, then find out and deliver what they want. There should be no need to try to "hide" anything. Just stick with the basics of taking good photos. Let them see what you've done, and make adjustments based on their feedback. Try to make them comfortable to minimize anxiety that may show through to the photos.