What portion of the universe is black holes? What portion of the universe is black holes? Is it possible to estimate the percent of all mass that is in the black holes?
 A: The cosmic inventory of the mass of various types of object is discussed in a well-known review by Fukugita & Peebles (2004).
They estimate that the fraction of the total matter in the universe that is made up of stellar-mass black holes (the final states of massive stars) is about 0.00025 with about a 30% uncertainty. A further fraction of about $10^{-5}$ is in the form of supermassive black holes at the centres of galaxies.
NB. These fractions are of the total (including dark matter). If you want the fraction of "normal", baryonic mass, them multiply these fractions by about 4.5.
As another answer correctly points out, a candidate for dark matter is primordial black holes, formed in the very early universe. Since dark matter makes up about 82% of the matter in the universe and no dark matter candidates have yet been identified, then it is possible that primordial black holes make up 82% of the matter in the universe.
A: This is an open question. We don't know. It's somewhere between 0% of the critical energy density (negligible) and 27% (all of dark matter).
At the risk of giving an answer way more complicated than you are looking for, check:

*

*Wikipedia on dark matter. Black holes would be a form of dark matter.

*There are ways to detect black holes. Naturally the most massive black holes are the easiest to detect, but smaller ones (so-called MACHOs, or Massive Compact Halo Object) can still be detected with microlensing.

*But this is imperfect because at some mass black holes become too small to detect. For example, an asteroid-mass black hole at the distance of Neptune from the Sun would be practically impossible to detect - the mass & radius are just too small.

*But in that case, it becomes possible that all of dark matter are tiny black holes. The major challenge would be "how did these little black holes form?", and the only real explanation is that they are primordial, i.e. they formed from density perturbations in the very early universe.

*But we have no idea how massive primordial black holes are, or if there are even any around. The theory behind density perturbations in the very early universe is not sufficiently well developed. Maybe primordial black holes exist and account for all the dark matter, in which case the answer to your question is 27%. Or maybe there are no primordial black holes and dark matter is made of WIMPs or axions or something else. In this case the answer is approximately 0%.

So the tl; dr is: we don't know, and the possible range is very wide.
A: As a point of interest, there is a theory that proposes that the extra mass in galaxies we call "dark matter" is actually small primordial black holes.  This theory has not yet been entirely excluded by experimental evidence, but it's quite difficult to prove since the hypothetical black holes would be smaller than the size of the moon and not densely distributed throughout the galaxy.
