How to evaluate undergrad CS programs when eventually aiming for PhD?
Although I'm sure you already realize this, you shouldn't let a laser focus on your daughter's professional development control her choice of which school to attend.  (Influence, sure, but not control.  And yes: HER choice.)  Given your daughter's background and experience, she will likely be very successful no matter where she enrolls.  I've seen very successful theoretical computer scientists come from a huge variety of undergraduate programs, not all of which were associated with strong graduate CS programs.  It is at least as important for her to find a place where she feels (and not just is) supported and challenged, both by her faculty and her peers.  Otherwise, no matter how strong the department is on average, it won't be a good fit for her personally.

There is absolutely no substitute for a personal visit to each campus, if you can manage it.  Let her drop into the comptuer science department, get a feel for the community vibe, sit in on a class, talk to a professor or two if she can, hang out in the dorms.  Meanwhile, you go somewhere else.  Go'way.  Shoo.

But if you really want hard data, I recommend that you—or better yet, your daughter—directly contact the computer science departments at the schools where she's been admitted, describe her experience and her goals (which should make them very eager to attract her), and then ask questions like the following:


How many students graduated from your program in the last five years?
How many / what fraction of those students are currently enrolled in strong computer science PhD programs?
How many / what fraction of your current undergraduates are involved in research with your faculty?
How many of your faculty do research in theoretical computer science?
[The Hail Mary:] Would you mind asking one of them to contact me?  I'd like to ask some more questions.


Beware the answer "I don't know", or qualitative waffle like like "quite a lot" that really mean "I don't know".  Ask for numbers.  Ask for examples.  Channel your inner Cuba Gooding Jr: Show me the data!

Your first contact will almost certainly be answered by someone on the administrative staff, who may not have the data you want at hand.  Be prepared make an appointment to speak over the phone (or Skype or whatever) with the director of undergraduate programs or another faculty member.  If you do speak over the phone, try to keep your conversation short and to the point; these people are very very busy.

Don't bother asking admissions officers these questions; Chances are very high that they just don't know.  You really need to contact the departments directly.

Another good place to look is the list of current and past winners and runners-up for the Computing Research Association's Outstanding Undergraduate award, which specifically recognizes undergraduate research.  A significant fraction of winners did their undergraduate research in theoretical computer science.  Also, a significant fraction of winners were not enrolled in departments with a top-10 graduate program. 

But as Anonymous Mathematician notes in a comment, you shouldn't take the CRA list too seriously; some departments are more interested in awards like this and push hard for their students to be selected.  The fact that some prominent departments have few or no students on this list may reflect a disinterest in this particular award, not in undergraduate research in general.

[I'm a theoretical computer scientist at a top-10 CS department; I serve on my department's graduate admissions committee.]