Is it permissible to develop a website concerned with student affairs, designing only the noble parts and leaving the "unseemly" parts to the website owner, knowing that the homepage will link to these parts?

It is permissible to work in website design, provided that the websites are free from prohibitions, such as advertising for them or promoting what involves sin and aggression. This is based on the Almighty's saying: (And cooperate in righteousness and piety, but do not cooperate in sin and aggression) [Al-Ma'idah: 2]. And based on the Prophet, peace and blessings be upon him, saying: (Whoever among you sees an evil, let him change it with his hand...) [Muslim]. Therefore, it is not permissible to include links or sections that invite to disobedience. The work must be limited to what is permissible, while advising the website owner not to add anything that angers Allah the Almighty. If he adds them himself, there is no sin upon you. However, if you refrain from dealing with someone whom you believe will add objectionable content, it would be better for you.