How to prevent regmatches drop non matches?

use regexec instead, since it returns a list which will allow you to catch the character(0)'s before unlisting

 R <- regmatches(x, regexec("a+", x))
 unlist({R[sapply(R, length)==0] <- NA; R})

 # [1] "a"  NA   "a"  "aa"

Staying with regexpr:

r <- regexpr("a+", x)
out <- rep(NA,length(x))
out[r!=-1] <- regmatches(x, r)
out
#[1] "a"  NA   "a"  "aa"