I've been rolling both of these round in my head for a while, trying to find different contexts where the usage might favour one rather than the other and essentially they mean exactly the same thing.
"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!
The first is not natural. The -ing form works only if the subject is actually doing something (or having something done to it):
It's nice to see Emma making new friends.
It's nice to see the prime Minister listening for once
It's nice to see this site being visited by so many people.
The second form has an ellipted that.
It's nice to see [that] this site has more than 5,000 members.
HAVE (in this sense), is not used in the progressive form.