I'm having trouble with the last update on my RPi3, but I've managed to solve it myself. I'm reporting this here, just in case someone has the same problem:
Since the last update, 04-04-19, I was having a very low performance on some 3D emulators, for instance, PSX one, barely having 3-5fps ingame on any game, even on "easily emulable" ones like Castelvania.
I have the feeling that libretro core isn't working fine, or that it's using armhf one. So I downloaded the last core from libretro nightlie's server (linux/armv7-neon-hf), and replaced it using WinSCP. Just copy the downloaded pcsx_rearmed_libreretro.so file and replace it on /tmp/cores/. Then fully reboot the Pi, and you are good to go.
Please, for future releases, please look into this. I assure the performance lose is big.
Thanks for your time, and forgive my english