I think this bears repeating, it's the principle point. These towns were not that big, and the militia often included many of their most prominent citizens, their merchants in the cavalry and their skilled craftsmen in the infantry. If a town of 10,000 people deploys 2,000 militia and loses half of them to dysentery in a siege, they have just lost 10% of their economy, and probably the most productive 10%.
I think it was kind of the opposite. They had a lot of speciality troops in the sense of siege engineers and the like, (though not as much cavalry) but what they lacked was cannon fodder, for the reasons you referred to above.you may not have one or more specialty troops (cavalry, siege engineers, etc), or you may simply need more troops than you have.
To underscore this, some facts: we have detailed records of the muster of a small army from the German city of Regensburg which went on campaign in 1431. The force consisted of 73 horsemen, 71 crossbowmen, 16 handgunners, and a mixed group of smiths, leatherworkers, a chaplain, pike-makers, tailors, cooks, and butchers, for 248 men in total.
This small force had a large number of supplies:
They brought 6 cannon, 300 lbs of cannonballs and 200 lbs of lead shot. Forty one wagons carried powder and lead, 6,000 crossbow bolts, 300 fire-bolts, 19 handguns, cowhides, tents, and horse fodder for six weeks. Supplies for the 248 men included ninety head of oxen, 900 lbs of cooked meat, 900 lbs of lard, 1200 pieces of cheese, 80 stock-fish, 56 lbs of uncut candles, vinegar, olive oil, pepper, saffron, ginger, 2 tuns and 73 “kilderkins” of Austrian wine, and 138 “kilderkins” of beer. The total cost of this campaign was 838 guilders. The source for this is the Osprey book German Medieval Armies, page 10.
This small, very well supplied force then merged with two other larger forces consisting of peasant levies and mercenaries, to the tune of about 1,000 more troops, mostly armed with polearms and lighter crossbows. This is a good example of how a hard core of militia, which had plenty well-trained, well-equipped specialists, a lot of times was fleshed out with more warm bodies.
Of course the opposite did also sometimes happen where the towns provided the 'cannon fodder' and the mercenaries or nobility supplied the specialists, particularly cavalry. These types of scenarios usually happened when the town was the lesser partner in a given alliance. But for the towns themselves, to the extent that they were in control of a given campaign, it was much more in their interests to try to get the most out of their expertise and special equipment, while reducing the risk to their population and therefore economy as possible.
G