I noticed that the RB2011 series routers are more expensive than the hEX RB750Gr3, despite having worse performance and one less internal gigabit link to CPU.

The things that come to mind that could make the RB2011 more expensive are the extra 100Mbit ports, higher RouterOS license level and more system drive capacity. However I'm not sure if those features are useful enough to choose the slower more expensive router.

Are there other things that I'm not noticing that could make the RB2011 a better choice for certain scenarios? Does it have better reliability or longevity? Is there any scenario where the hEX should not be used but the RB2011 could be used (instead of a better router such as RB3011 or RB5009)? The question is about non-wireless RB2011 versions only.

Well...I think it was introduced around 2014, I think you can say the RB2011 is reliable on the long term.
But instead of thinking about the differences...what are your requirements?

I'm currently using a hEX, but considering an upgrade to something future-proof that can fit in a 10" rack. I'm not considering the RB2011 for that and I'll likely just go with RB5009. I was just curious what makes the RB2011 more expensive than the hEX when it doesn't seem like a better choice when just looking at the specs.

Higher production costs? And there still seems to be a market for it.

The question is, why is there a market for RB2011 if hEX exists? What makes RB2011 a better choice for those who buy it?

Is it just the higher license level, 100Mbit ports and disk space?

I also noticed RB2011's gigabit switch has a rule table but hEX doesn't, maybe that's the selling point?

Less components, lower costs.

So, at the end ??

At the moment (hopefully not the end) for roughly the same money you can get a L009 (which is - or should be according to Mikrotik - the "natural" successor of the RB2011) :
https://mikrotik.com/product/l009uigs_rm
119 US$

The RB5009 is in another category, both in performance/features and cost.
https://mikrotik.com/product/rb5009ug_s_in
219 US$

The RB2011 is discontinued.