They didn't find the Intrepid.
They didn't look for her at any point.
It's pretty clearly spelled out that she was eaten by the amoeba.
But so was the Enterprise. No harm came to her from that - only to her crew and her power supplies.
Frankly, I was surprised that the TOS-R team didn't insert some identifiable wreckage as the Enterprise was cruising through the protoplasm.
The thing would have been too big for the two starships to end up within visual range of each other by accident. Visual range being not particularly long in that soup...
From Spock's comment that the crew of the Intrepid didn't understand what was killing them suggests to me that they died prior to being within visual distance of the Space Amoeba.
Neither Spock nor McCoy seemed to be understanding what was killing them, either, despite definitely being within visual range of the beast...
The Enterprise, in some way, did "something" different than the Intrepid. Kirk made a decision different than the Vulcan Captain did, or the Enterprise possessed stronger shields, or the Enterprise slowed down where the Intrepid sped up.
Seems so. Although our heroes never suggested there would have been a difference in the capabilities of the two ships; Kirk assigns the continuing survival of our heroes to the fact that they're acting differently from Vulcans, cruising through the illogic of their situation by virtue of being natural illogicians themselves.
Might be the amoeba killed the Vulcans with a trick we didn't see it use against our heroes. Might simply be the Vulcans tried out some logical trick for blowing up the beast, and ended up blowing up themselves and being astonished by that fact for a fraction of a second.
Timo Saloniemi