I've played BG since vanilla and have been partial to a Kensai since my first crack at BG2. Originally it was the Kensai/Mage, but coming back to the game in recent years I prefer a straight Kensai.
I have the GOG games installed - both EE versions, unmodded, and BGT with SCS and a few Tweaks installed. To my surprise, in both installs I have found my kensai nerfed because the ioun stones and Strohm's mask no longer protect against critical hits! Sadly I have decided that it makes a no-reload run unviable unless you sap all the fun out of it and have your kensai throwing daggers from the back.
This change only to seems to affect pure kensais and thieves who have no other ways to defend against critical backstabs - a nontrivial threat in SCS - which will end a no-reload run right quick (or, almost as frustratingly, perma-kill Yoshimo in chapter 2).
I assume that the change in both versions represents a community consensus, and a quick Google produced what amounted to an RP argument to the effect that "a little stone whizzing around doesn't actually protect your head".
So my options are "don't play a straight kensai" or "mod the game". I've chosen option 2, but would humbly propose that this should be standard. If the only argument is based in physics, the RP solution is simple: defence against critical hits can be part of an ioun stone's enchantment. The text for the items stones could be updated to reflect this.
I would even be happy with a compromise position that *some* stones - those suitable for a front line fighter - would be enchanted to include critical-hit protection. Pale Green and Wong Fei seem like the obvious choices. The extra HP could be eliminated in favour of the crit protection.