Until a reliable, independent news agency verifies it, any claim from either side should be viewed as misleading. It's also worth noting that it's not just Hamas denying this, it's also the facility itself. Here's part of a report from one of the BBC correspondents in Gaza:
"Israel has accused Hamas of having a command and control centre underneath Shifa - which the group denies.
I have been to the hospital hundreds of time - I was born there, my son was born there, in the last two months of my mum's life, she was inside the kidney dialysis centre and I used to visit her every day.
It is very hard to verify what is underneath. With my eyes, I haven't seen any military capability inside the hospital buildings."
Lastly, consider the fact that this hospital is in one of the places the IDF instructed Palestinians to flee to . Are we now saying that the IDF were purposefully trying to place Palestinians in danger by telling them to go to a location where they knew Hamas operated from?
The BBC quote Dr Ebrahem Matar, a heart specialist in the intensive care unit at the Aqsa Martyrs' hospital - the only medical centre in the middle area of the Gaza Strip.
"Dr Matar said there was only one operating room and limited number of staff.
"'It is catastrophic and it is difficult. We see patients deteriorate due to the continuous pain and the continuous resistant infections.
"The hospital is in one of the areas the Israeli army has told Palestinians to flee to.'"
EDIT: It looks like this is a different hospital Dr Matar was talking about. I'll update my other comment too.
Here's a map from the BBC, the area 'Wadi Gaza' is one of the areas the IDF told Palestinian's to flee to - Dr Matar's hospital (Martyr's) is in that area.