A: It is great that you are concerned about being tactful with your boyfriend regarding his son!
The best person to ask whether this child should be encouraged to give up his pacifier to improve his teeth or his speech is the child's dentist or pediatrician. Then the answer is individualized and based upon science. A professional recommendation won't hurt anyone's feelings.
But an important part of your question is not about teeth but about your overall relationship to this little boy, and whether or not you take on the full role of daily caregiver as a parent would do—or what part of that role you may take on. This is an issue which you and your boyfriend can talk over. Probably the child's father would be relieved if you raise the issue in a kind spirit, asking him to tell you what his preferences would be in terms of your speaking up (or being silent) regarding all of your opinions about how to help raise this little boy. As his father, he may welcome your teamwork in being a parent. Or perhaps he may not! A discussion of what role he expects you to play and what role you want to play might clear the air for many future issues.