Normally there's no point in stealing usable F-16 and F-15 engines because the engines, and many of their parts, have serial numbers that are regularly tracked. But as scrap, and untraceable spares, the engines can be sold into the black market. The recent theft was also apparently for the purpose of selling the engines for components, as illegally selling intact engines would be too dangerous.
It’s not just F-16 parts that are disappearing from Israeli bases. Earlier this year seven Bedouins (who are often involved in smuggling) broke into a poorly guarded army depot and made off with 3,000 tank gun shells (worth over $6 million). The shells were sold for scrap and fetched far less cash. The Bedouins were caught and prosecuted. The army promised to increase security on the many storage sites for weapons and ammo scattered around the country.