Danke schön!

#1 ganz sicher nicht.

It was nice to have you here ist schon okay. (It was nice having you geht aber auch, glaube ich)

#3: Motzen ist leicht; es besser machen offensichtlich nicht.

It was nice having you here

is fine, there's no had in there

@Werner: why don't you for once shut the eff up!

Ich habe es so schnell abgeschickt, damit Carita es noch sieht, bevor sie deine Antwort übernimmt. Wie du siehst, habe ich meine Antwort dann nachgeliefert.

Im übrigen ist auch ein Hinweis auf etwas Falsches hilfreich, wenn man selbst keine bessere Idee hat. Deshalb kann man ja trotzdem verhinden, dass jemand Unsinn schreibt.

I agree with Gibson and dude. "It was nice having had you here" does not sound idiomatic. You could probably construct a situation in which that tense would be okay, but it's not the garden-variety thing to say.

Options:
I'm glad you could come.
It was nice having you here.
It was so nice/wonderful/good to see you.

Less formal:
Thanks for coming.

If the company spent the night at your home:
I'm glad you could come and stay.
I'm glad you could visit.
It was nice having you here.

Disclaimer: All the above are AE. Quite possibly BEler have a charmingly different way to say it.

No, we just say it the same way.

The problem with 'it was nice having had you here' is that it puts the stay too far into the past; it would mean that you enjoyed their visit when it was just finished.

http://www.bearforum.com/cgi-bin/bbs4.pl?read...
Bill, always a pleasure having had you with us

http://localism.com/neighbor/561homesource
It was a pleasure having had you as a real estate agent

To cite just a few.

The text is ambigious. It can well mean that the stay is over and the sentence fell a few days/weeks later.

http://www.bearforum.com/cgi-bin/bbs4.pl?read...
It would be illuminating to quote more of the context from that source. The sentence directly preceding reads:
"Maybe in hindsight I better had passed on being a bear untill they finally hand him the pink slip?"
which is (also) wrong English.
Just because someone somewhere writes something on an internet forum doesn't make it correct.

It can well mean that the stay is over and the sentence fell a few days/weeks later.
That's not the point, though, Werner. You're saying that you enjoyed the time immediately after their stay, not that you enjoyed the time of their stay.

Having had a bath, I blow-dried my hair ---> safe
Having a bath, I blow-dried my hair ---> dangerous

"It was a pleasure having had you as a real estate agent. I will certainly send referrals your way. Daniel and I realized the other day how good you were through the process, and that we would not have been able to find our dream home as quick as we did if we did not have someone like you on our side.
http://localism.com/neighbor/561homesource

---> if we had not had someone

we really enjoyed your visit
it was great that you visited (us)