Why are Davis & Main's perks so much better than HHM's?

We have no means of comparing the two companies' revenue.

The fact that D&M is in a smaller city doesn't necessarily mean the company has lower revenue. The city may be wealthier, and it may have more higher-end businesses and clients. D&M may be a bigger fish in a smaller pond, or the only big firm in Santa Fe, whereas HHM has to compete with other large firms like Schweichert & Cokely. The cities are very close together, so there is probably overlap anyway. In short, there is not enough information to support your assertion that D&M has fewer/less lucrative clients or less revenue than HHM.

Company perks are not tied solely to the company's revenue--the boss's personality matters.

Company perks are decided upon by the partners in that company, which gives a lot of leeway to personality. Unlike Howard Hamlin, Clifford Mains is depicted as quite caring about his employees and overall more of a laid back kind of person (e.g., he plays guitar in his office). Mains is also depicted (and described by others) as very socially conscious. Yes, he is a business man, and a serious one at that, but he is depicted on the show as the kind of boss who would tend to be more giving in terms of perks than Howard Hamlin or Chuck McGill. It should come a little surprise that D&M is perhaps more generous with its perks.

HHM perks are not necessarily as far behind D&M as you suggest.

What are the perks of D&M?

1. A company car - most law firms provide company cars to their lawyers and allow them to buy them when they leave. Kim had a nice car when she was at HHM and could have purchased (or picked up the lease) it when she left. Kim did not drive a German car like Jimmy, so D&M was maybe more generous in what it allowed. Or maybe Kim was more modest in her tastes.
2. A signing bonus - this all depends on the lawyer and how bad the firm wants them. HHM might definitely give a signing bonus to a lawyer they really wanted.
3. An apartment - Lots of companies arrange corporate housing for high level hires coming in from out of town (Jimmy was from a different city) so they can hit the ground running and take their time finding a permanent home. This was a temporary perk, not something the company provided everyone. HHM might do the same if it hired someone from outside ABQ.
4. The spacious office - D&M seemed to have much more spacious office spaces, but this is a function of the architecture in the building selected by the partners. Again, this goes to the personality of the boss.
5. The desk - Jimmy's Cocobolo desk (and the ease with which his assistant got it) suggests a generous employer who really wanted Jimmy to be happy. It is hard to imagine HHM doing the same. This is the one perk that stood out as something HHM wouldn't do.

Overall, the perks at D&M are probably comparable to those at HHM, with the differences being a function of the senior partner's personality more than any other factors. Remember also that the personality cuts both ways. Nobody at HHM would pester you about where you throw your soda cans, for example. The main reason D&M's perks loomed so large is that Jimmy was the one getting them and it is his perspective that dominates the show.