The Dark Forest problem posits that in the time required to send a message to a distant civilisation, the sender could just as easily send something that would destroy the distant civilisation. Further, that it is not possible to know without communication whether a distant civilisation would have peaceful or belligerant intent. Therefore, any civilisation that knows the existence of another should pre-emptively destroy the other rather than risk waiting to find out if it is peaceful

If FTL communication is possible, it could be possible to establish the other civilisations intent before they could send anything destructive.

As for the Sophon's it might be that they require a compatible recipient to work and so first require matter to be sent to the distant location. It's a long time since I read the Three Body books, but I seem to remember them being based on quantum-entangled particles, which would fit with this.