I don't know for sure, but I assume (on the basis of what you have said in other threads) that EMBOSS is a gene sequence manipulation program/suite.

Given that genes sequences tend to be represented by pairs of chars, it quite probable that the routine you mention shuffles pairs of bytes around.

It's also quite likely, though again I don't really know, that this would be done in C, which is probably much faster that any implementation in pure perl. Though it's possible that one of the modules above implements the shuffle using XS or C in which case they could be comaparable for performance.

In terms of "true randomness", provided the shuffle is reasonable well written, the randomness will come down to the randomness of the RNGenerator, and unless your involved in crytoanalysis or heavy statistical analyisis, the RNG on most systems is good enough for most purposes.