The EMH was an emergent intelligence, made so by leaving his program running and allowing him to expand his programming.
From
The Swarm:
ZIMMERMAN: Here we are. A schematic of the EMH and it's component sub-routines.
EMH: Can you determine the source of the problem?
ZIMMERMAN: This isn't good. The EMH has a level 4 memory fragmentation. How long has the program been active?
EMH: I have been active for, for
TORRES: Almost two years.
ZIMMERMAN: Two years? Well there's your problem. This program was developed as a short term supplement to your medical staff, fifteen hundred hours tops.
TORRES: I know. I added data compression buffers to compensate for the additional time but they're breaking down.
ZIMMERMAN: The EMH is a highly sophisticated program. You shouldn't go meddling in it's matrix when you don't know what you're doing.
TORRES: Should we shut down his program then till we figure out how to fix him?
ZIMMERMAN: At this point it doesn't matter. With a level four memory fragmentation it'll simply continue to degrade. There's only one course of action - a system-wide re-initialisation. Start over from scratch.
TORRES: We are aware of that option. Would it be possible to expand his memory circuits instead?
ZIMMERMAN: Of course. Schedule it for your next maintenance layover at McKinley Station.
TORRES: I'm afraid that is impossible. We're thousands of light years from Federation space.
Zimmermann: Well, there's nothing more I can do. Either reinitialise it or live with the knowledge that eventually this EMH will end up with the intellectual capacity of a parsnip.
After two years of continued use, the program was already failing. They saved it with drastic measures. At the very least each EMH would need its memory circuits expanded in order to survive its own limitations.
By
Lifeline, when he revisits Doctor Zimmerman, the EMH had been running continuously for
six years.
My point: those laboring Mark I's were most likely not left running continuously nor allowed to expand their programming. They were more likely used as originally intended - in a part time capacity. As such, they would have never had the opportunity to exceed their programming. They were, in fact, tools. The Doctor demonstrated that individuality could emerge from that state, given the capacity for memory expansion, experience, learning, and change.
The fact is he was never anything more than a collection of circuits that became very good at reproducing a mind experiencing the world. Perhaps he even became self-aware. (Saying so and being so are two different things). He was, for all intents and purposes, an autonomous, intelligent being, capable of growth, relationships, and self-reflection.
The Mark I's were not slaves. They were potential individuals, but they were not individuals. They weren't even supermarket eggs.
In order for them to be individuals, they would have each had to undergo similar extreme alterations as the EMH. They were equipment, not a class of sentient beings. Nowhere does the canon state that they underwent any alteration from their original programming.
ZIMMERMAN: ...I tried to have them decommissioned, but Starfleet in its infinite wisdom overruled me and reassigned them all to work waste transfer barges....
Reassigned. Not reprogrammed. Not reconfigured.
Also - even on his best day the EMH might not even be a life form at all, but an analog of one.