As someone who was responsible for the cleaning of the softserve/milkshake machine at a fast food chain while working through uni - I wouldn't. I must admit that I don't follow the do not eat list particularly well when pregnant but this is one food that, because of my experience, I definately avoid.
The machine does have a steralisation process that is run every night but, where I worked, the actual machine wasn't cleaned more than once every fortnight (pulling everything apart, scrubbing it down etc would take me at least 2-3 hrs every fortnight). You might actually be able tell when a machine is next due for a full clean - each machine has a lcd screen somewhere on the front that lists the temp of the mix and the date for the next clean - it just depends on how the machine is positioned compared to where you're standing/how good your eyesight is.
Where I worked they had a guideline that the mixes weren't to be topped up the day before it was due to have a cleaning but this was often ignored. I would be told to empty the mixes into huge buckets and store them in the cold room while I cleaned the machine. Once I'd scrubbed down all the parts and put the machine back together I would have to put the mix that I'd removed earlier back into the machine so, if there had been any contamination, it was just going straight back into my clean machine.
Don't get me wrong, I love my sundaes and have them on a semi-regular basis when not pregnant but its one thing that I'm not willing to have when pregnant because of what I know having worked in a fast food store and being directly responsible for the manual cleaning of the machine.