Are too many function calls bad(as in slows speed performance) for programs written using interpretor-based scripting language(JavaScript, Perl)?
Practically speaking, function calls have a cost.  They have a cost if your language is interpreted.  They have a cost of your language is compiled.  Some compilers can substitute the code for some functions (it's called inlining), but in the vast majority of cases, one does not do that.

However, the cost of a function call is low.  If you have a 50 line function with a reasonable amount of work done on each line, you'll find function calls account for less than 1% of your total runtime.  Their value in organization typically far exceeds their cost.

You don't want to be excessive with function calls unless you can inline them.  Some styles of code depend on inlining, such as some C++ code which may have 10+ function calls nested and do perhaps 3 lines worth of work.  That kind of a situation demands inlining.  However, for the vast majority of the cases, don't worry about it.

You will eventually learn how to profile your code, which is a way to find hotspots where you spend a lot of your time.  Always profile before you optimize.  You will find that most of your function calls don't have a significant effect on runtime at all, and if you're unlucky, 3-4 functions might have too much overhead.  Then you remove those functions, inlining the code manually, and you leave all of the other functions.

If you're interested in numbers, it is estimated that a function call in Python (an interpreted language) costs between 150ns and 350ns.  In C++, the cost is on the order of 15-30 instructions, which is on par with a L1 cache miss (if that term doesn't mean anything to you, it's a good indicator of just how fast these function calls are).  On a 4GHz processor, that's 4-8ns.