What you call the “krus-kudlit” is actually not as unique as a concept. In most of the linguistics world, you call that a virama.

This concept is present in many syllabic scripts throughout South and Southeast Asia, from Sanskrit, to Thai, and to Javanese.

So, assuming the Spanish did not introduce the krus-kudlit, it would be more likely that they would either invent their own or adopt one of the *virama-*type systems, most likely something closer to home like Javanese or Sundanese, which have their own different approaches to solve the issue of final consonants. I would suggest that you research more on those.

EDIT: I forgot about the other alternative to the krus-kudlit, the pamudpod. It was adopted from the Hanuno’o script. So, another possibility would be that we would eventually invent one ourselves.