How are "expect" altitudes on STARs used?
My questions are:
  
  1) When you enter the STAR in the the FMS, will it pre-populate the expected altitude, and does this show up in the FMS exactly the same
  as a mandatory crossing altitude?


This depends on the model of FMS.  Some of them don't even have Vertical Navigation (VNAV), and it really depends on the exact model.  I will say that three of the most common FMS's that I have personally used (Universal, Collins, and Honeywell) all pre-populate the expected altitude and it shows up exactly the same as a mandatory altitude.

In any case, the FMS is advisory only.  Unless the pilot dials in the actual assigned altitude and selects a vertical mode on the autopilot, it isn't going to descend on its own.  So if ATC doesn't assign the crossing restriction, you may see your VNAV pointer come alive and watch as you fly through the vertical profile without capturing it and it would be perfectly normal.  If I am getting close to the point where I would like to descend to make a crossing restriction and haven't been given lower, I will sometimes ask the controller:  "Do you need me to make the crossing restriction at RUGBB today?".  This gives me an idea of what's to come or prompts them to give me the descent clearance.


  2) Are expected altitudes treated as suggestions by pilots or controllers? For example, in the above chart, if you were at JHAWK
  15,000ft landing south, and Kansas City Center or Approach told you to
  "descend at your discretion, maintain 8000", would you (or the FMS)
  make any attempt to cross RUGBB at 12,000 even though it's not
  required?


An "expect" altitude is just that.  It is an altitude to expect, but it is not always actually assigned.  If it isn't, then you don't have to make it and since your example is at pilots discretion, you could descend at whatever rate you want.  You could cross RUGBB higher or lower than 12,000 ft and nobody would care.

In actual practice, they usually only do this in a few situations:


If they have to hold you up higher due to traffic and you can no longer make the crossing restriction, they will just give you a "descend and maintain" altitude, sometimes with a "good rate" tacked on.
It's a particularly slow time (late at night, etc.) and there isn't much other traffic to worry about.
There is an aircraft at, say 13,000 ft. so they tell you to descend and maintain 14,000 ft with the intention of giving you the crossing restriction once you pass the conflicting traffic.


In this last case, I would get down to 13,000 ft. in time to make the crossing restriction if they gave it to me, but it wouldn't be required.


  3) How common is it for ATC to actually issue a "cross [fix] at [altitude]" where the fix and altitude are as expected on the chart?
  And, if it is common, why wouldn't it simply be mandatory?


Again, this depends on the procedure but it is quite common.  That's why they put them there so that you can plan on what is typically done.  There may be operational reasons (like two different procedures that intersect) which prevent them from issuing it every time, so they can't just make it mandatory.


  4) Are expected altitudes part of lost communications procedures?


Surprisingly, no.  Not unless the controller has specifically cleared you to expect or cross it or "descend via" a procedure.


  5) Am I missing anything with regards to the purpose of expected altitudes?


Not on this one!  In some cases, there is a speed restriction which is listed on a separate line from an expect altitude. In these instances, the speed is required whether or not the speed or altitude was verbally assigned, just by being cleared via the arrival. For example, on the SFO HADLY2 arrival, you are required cross EUGEN at 250 knots, whereas 11,000ft is only required if assigned by ATC.