Hello native English speakers.
1. No matter what topic they talk about, they can talk to whoever they want. We encourage this kind of behavior of theirs.
2. They are encouraged to speak with whom they will on any subject.
Query :
Do both have the same meaning? and, are both grammatically correct?
Which is slightly better?
3. They are encouraged to speak with whom they will on any subject.= （I guess）They are encouraged to speak with whom they will speak on any subject.
Is my guess correct?

Question

Hello native English speakers.
1. No matter what topic they talk about, they can talk to whoever they want. We encourage this kind of behavior of theirs.
2. They are encouraged to speak with whom they will on any subject. 
Query :  
Do both have the same meaning? and, are both grammatically correct?
Which is slightly better?
3.   They are encouraged to speak with whom they will on any subject.= （I guess）They are encouraged to speak with whom they will speak on any subject. 
Is my guess correct?

Answer

They're both grammatically acceptable but not as clear & efficient as they could be.

I would favour option 1 if explaining to a child, or someone who is struggling to understand, especially if I'm in no hurry. Option 2 is better for official formal usage where time should not be wasted, as it's more concise & tidy, but requires a slightly higher level of English to understand.

Your guess is correct.