Can Emacs org-mode be used to createToDo's linked to a line in a LaTeX source?

org-insert-link is your friend in this. Bind it to a useful key globally, like C-c l, which you can use in your LaTeX file under AucTeX. The anchor inserted by org-insert-link isn't exacly permanent if you mess with the file enough, but it works most of the time.

A different solution would be to write your thesis in Org, including the ToDo's, and export to LaTeX.

Here's an MWE, except the link won't work because you don't have the LaTeX file I'm linking to.

#+TITLE:     Some links to a LaTeX doc
#+OPTIONS:   H:3 num:t toc:t \n:nil @:t ::t |:t ^:t -:t f:t *:t <:t
#+OPTIONS:   TeX:t LaTeX:t skip:nil d:nil todo:t pri:nil tags:not-in-toc


* This is an ordinary heading

This is a link to a context in a \LaTeX{} file with
[[file:~/Dropbox/_support/LSM2241/L7/LSM2241-AY201213-S1-L6-Feedback.tex::\section*{Q6%20How%20can%20the%20delivery%20of%20the%20material%20be%20altered%20to%20enhance%20your%20understanding%20of%20the%20material?}][some
helpful linky text]]. Note that the link keeps a bit of context,
which is created by running ~org-store-link~.

I have org-store-link globally bound to ~C-c l~ in emacs. Once the
link is stored, just insert it with org-insert-link


* TODO [#B] Finish this section

This *TODO* heading prints the *TODO* mark when the ~todo:t~
property at the top of this file is enabled. The template is
inserted with ~C-c C-e t~

* But honestly?

Why not just write your thesis in Org and export to \LaTeX{}
instead of keeping separate files?

From the Orgmode manual:

file:sometextfile::NNN                    file, jump to line number
...
file:projects.org::some words             text search in Org file

Even though the manual talks about searching "org files" for the latter case, if you link it to a non-org type, it will do a text search. That's what @GTK's example uses.