"It's nice to see this site having more than 5,000 members" is a contraction of the present continuous tense ("is having") and "It's nice to see this site has more than 5,000 members" is the simple present.
The only shade of difference I can think of if if the next sentence goes on to qualify this in some way - particularly if it's a negative or sarcastic comment.
For example, "It's nice to see this site has more than 5,000 members - there's no way this is going to last!" sounds fine. But to use the continuous tense (is having) wouldn't be appropriate if the implication was that this state of affairs is unlikely to continue!
Student or Learner