and iterate through all the hash keys

Don't ever iterate hash keys! (Well, hardly ever :)

The major purpose of hashes is that you can lookup the value associated with any key directly, avoiding iteration.

For your purpose, the major part of the code should be something like:

while( <$names_to_be_replaced_file> ) {    ## read each line
    s[\b([a-z]+)\b][ $name_id{ $1 } ]ge;   ## find words, look them up
+ and replace them with the id
    print;                                 ## Send the modified lines 
+to stdout
}
[download]

Simple and very efficient.