In a matter-antimatter reactions, absolutely ALL matter (100%) is converted into Energy? If not, how much % is? 99.9999...%?
When a particle interacts with its antiparticle, a number of things can happen depending on the energy of the two interacting particles, and their masses. Annihilation means that all the quantum numbers that distinguish the particles add up to zero. If the energy in the center of mass is not enough to create a different pair of particle/antiparticle the total energy of the system will go into photons.
As neutrinos have very small mass a pair with of antineutrino/neutrino would have a probability to be created in electron/positron annihilation if the electrons have some kinetic energy. For higher energy electron/positron annihilation, as in LEP experiments, the energy can go to pair creation ( to conserve quatum numbers) of all the possible elementary particles and their antiparticles, as well as gauge bosons.
In the case of proton antiproton annihilation, even if they are practically at rest, a number of bosons ( pions) are produced.
The antiproton generated in the decay of an antiLamda generates a lot of pions (the star of tracks) in annihilating with a proton in the bubble chamber.
So all the energy( including the incoming kinetic energy) in the annihilation of particle/antiparticle for high momentum beams goes into massive particle antiparticle pairs, bosons, so some of it is mass , and some of it kinetic energy of those masses. It needs quantum field theory to calculate the percentages and probabilities of the various reactions so a simple number has no meaning.
So if you are thinking of energy as contrasted to mass and kinetic energy, no only in very low energy electron positron annihilation mainly photons are produced, which may be considered the purest we have in energy.