Janeway is only a Captain.
On Voyager that might seem like a big thing.
But there are thousands of Starships in the fleet.
EMHs could be worse than tribbles is they are allowed to breed without reservation.
And that's not even if they're all accidentally becoming self aware.
Besides,the problem episode is Message in a Bottle.
The Doctor goes to he Alpha quadrant and it is only after his program is shot across the galaxy that they begin to suspect that he might not ever come back and Harry tries to Build an EMH from scratch.
If the EMH was still on Voyager and Harry had to make a copy, sure fine.
I can copy a windows 8 installation disk easily, I have a few floating about.
But I couldn't make one from scratch.
In Message in a Bottle, becuase Harry didn't have the original to copy, he was frakked, but if he did, then maybe we might see how easy it is to mass produce these blighters... We don't know when they designed/built the back up module which we saw in Living Witness.
In Eye of the Needle they even said that he was integrated into the Sickbay so they couldn't back him and take him to Romulan space with the rest of the crew, but that was when they were all young and stupid.