So, the short answer to the OPs question is "Yes". If there is a tourney that is guaranteed to pay out $5,000, then that money will be paid out regardless. If they start off saying 15 spots pay out to start and only 15 people register, then yes, they all make the money.
Having said that, it is extremely rare to see a guarantee tourney not easily exceed the guarantee. From what I've seen, it would appear that 90% or more of the registrants sign up in the last 30 minutes prior to start (most likely because each poker site
spams their chat blocks at every single table).