Those ancient cities like the one in Turkey are quite compact and tend to have populations of 10-20,000 people.
It sounds like you are talking about the Türkmen-Karahöyük site. The stone found in a irrigation ditch by a farmer indicated that the nearby tell (mound) already being investigated might be the "lost" short-term Hittite capital of Tarhuntassa (or the capital of a briefly lived rival empire. Tarhuntassa was known from written records, but not located. The archeologists were already engaged in a broad survey of the whole region and specifically a more intense survey of the tell near Türkmen-Karahöyük which really, really, really looks like the ruin of an ancient city. (So many of these in the region are built-up dirt mounds.) Here is a fascinating talk about the diggings at the site and the inscription found nearby:
Basically, they knew there was probably an ancient city there for a long time, but hadn't performed a detailed dig, and didn't realize the possible importance of the site.
As for the Sinai...
It is similar, systematic surveys that I suspect the Israeli archeologists conducted will looking for the traces of the Exodus. (They were literally trying to prove that that part of their history was true in part to solidify their claim to Palestine based on the very next part of the text --- Joshua's conquests.) If they hadn't been thorough, I doubt they and more recent Israeli archeologists would be quite so firm about the absence of evidence claim I have repeated from them because I trust their expertise.
Only the coastal portions of the Sinai are dunes, in the rest, the standard techiniques of test trenches, etc. are feasible. For your reference I have included a link to a geological map of the Sinai (tan w/ dots is dune landscape), be warned that the file is large and loads slowly.
https://esdac.jrc.ec.europa.eu/images/Eudasm/Africa/images/maps/download/afr_egsgam.jpg