Can legitimised bastards be heirs

On your first question: disinheriting your heir is not possible unless you have elective succession. Then you change for example choose to elect your second or third son. Most of the time your vassals will elect the person you elect. Off course there is a chance they will elect someone else, so it's tricky.

On your second question: yes, it is possible. I have done it before (horrible me) when I was in kinda the same situation as you. My heir died relatively young and so his only son became my heir, but had really bad traits. So I plotted against my grandchild (who was about 4 years old) and managed to successfully kill him. There is a catch however, which happened to me. The plot was successful but the truth came out that I did it, so I got the Dishonorable trait and, even worse, the Kinslayer trait which gave me massive relationship penalty to my family and vassals. So yes, it's definitely possible but there are some serious risks.

It's worth noting that when the child is born your son will mistakenly believe it is his and act accordingly.

However there is a

• 'The husband suspects something ain't right'
• 'On-action event: Pregnancy in matrimony, with another father!'
• 'The father's wife is angered' events.

So there is still plenty of ways this can go wrong and ruin your relationship with your son. If the child does become your bastard you can choose to legitimise him though. I would see how the new childs attributes compare to your own sons. Then work out which one to favour. You can always have someone locked up if necessary.