1- What would be the best way to learn posix with focus on BSD's, shell and Perl?
I know that "books" (paper with printing on it, bound on one edge) is getting old fashioned. But about 20-25 years ago, O'Reilly had a really good set of manuals about Posix standards. I had the ones for the C library, real-time (threads + async IO Posix.4, book is by Bill Gallmeister) library at home, and used them as reference manuals when programming. If you only read documentation that's tuned to Posix instead of BSD- and Linux-specific man pages, you will likely end up with Posix-compliant code.
There are also Posix standards for the shell, including standard utilities such as sed and grep (don't remember about awk).
2- Is there another language for sysadmins besides shell and Perl?
Actually, the primary language is shell, because it is always there (on any machine, even in single user mode). It is also what a lot of the system's infrastructure is coded in. A good programmer and good sys admin has to be quite conversant in shell (and preferably not tcsh or bash, but real sh).
I would describe Perl more as a rapid development, interpreted programming language, not a scripting language. Today, a lot of that function is also taken by Python and Ruby.
Most sys admins do not program in C.
3- What is the best way to navigate the FreeBSD source code?
The kernel source code? Start by reading the "black daemon book": Design and Implementation of the FreeBSD, by Kirk McKusick et al. Only after reading the book, and understanding the structure, does it make sense to go into the source.
But the code itself is not very enlightening. You don't see the design principles and overall architecture by looking at lines of code, at least not right away.
4- What are the languages most used in FreeBSD development?
For the kernel itself, most utilities (sed/grep/...), and a significant fraction of packages: C. But as said above, also significant amount of sh.