Bit-parallelism and NFA simulation
on p4-5 of your 2nd ref by Faro and Lecroq they write:


  Online string matching algorithms (hereafter simply string matching algorithms)
  can be divided into three classes: algorithms which solve the problem by making
  use only of comparisons between characters, algorithms which make use of deterministic
  automata and algorihtms which simulate nondeterministic automata using
  bit-parallelism.


however, while sounding general, these statements seem to be wrt "within the realm of string matching algorithms". in other words there is massive use/ research of bit parallelism of NFAs for string matching algorithms in particular, but have not seen much bit parallelism ideas applied to arbitrary NFAs, even though it is clearly applicable. here are two refs turned up that do consider bitwise operations on a more general/ arbitrary case (apparently the focus of your question). in the 2nd case, "vector algorithms" are capable of/ nearly the same as "bit parallelism".


Implementing WS1S via Finite Automata / Glenn, Gasarch, sec 4, "internal representation of Automata"


  we do this with elementary bitwise operations

Fast Implementations of Automata
Computations / Bergeron, Hamel sec 2.2 "solving more complex automata"


  In this section, we establish a sufficient condition for the existence of a vector
  algorithm for an automaton.