Because, if I understand the design concept correct, you should rather expect to be ganked at these sites either by players or NPCs, so a high value covert ship is too high cost. These sites will be 'anomalies', not 'signatures', as such you need no probes to locate them. It has even been stated they will have their own color marking (not red or green) so you know immediately one is present when you enter a system. And time is of the essence here; you only got 5-20 (so expect 5) minutes to clear the site after the first person enter before the hackable containers explode (maybe damaging you) and a gank squad of NPCs appear. These have no bounties, probably no loot either but capable of dishing out a lot of damage.
As I think you can see, there is not much gained from using a SoE ship except for the added bonus to Analyzers. But you can get that from a tech 1 explorer ship too. I would prefer the speed and ability to get out of a hot place fast of the scout ship though.
I find the mechanic instersting and I expect both explores and lurking pirates to become victims of those NPC gank squads.
ADD: Oh, and of course; a scout ship has better combat capabilities to handle people in explore ships that might have arrived to the site before you or after.