Why use slow weapons?

For gemming/enchanting weapons there is a clear dps advantage to faster weapons:

dps = dmgPerHit / delay  
dps_gemmed = (dmgPerHit + X) / delay  
dps_gemmed = dps + X / delay  

where the term X / delay is larger for fast weapons.
Similar arguments can be made for stackable on-hit debuff such as -armor per hit or conveys dmg over time on hit.

My question then is why would we ever use a slower weapon?
Do they tend to have higher base dps to compensate or maybe some other effect I'm missing (aside from aesthetics)?

Slower weapon types are those which generally have a higher DPS as you guessed. These are the Hammers and the cannons that you know of. as per your suggestion, using gems on faster weapons does give you a bigger return. But at higher difficulty levels, the smaller(faster) weapons will not be very effective since the armor on the mobs increase. This is when higher DPS weapons shine, since you will be doing way more actual damage per hit than the faster low damage weapons.

But as for gemming goes, your theory is right. A faster weapon with a -X Armor per hit is a very potent weapon indeed. But it does mean that your initial hits will only be useful for reducing armor and the damage piles on later. It seems like it could work, but in reality at higher difficulties, you have to be careful about survivability since the mobs hit harder. You cannot afford to spend time getting hits to lower armor as this means spending more time avoiding/taking hits from mobs. You are better off outright killing them with high DPS weapons.

Hope this answers your question.