Hello sufflaminandus! First of all, I'm long time player but only recently tried my hand in an actual mod creation, so some things are not known to me as well. Here is, however, what I know.
1. What is your favorite approach in creating creatures (specifically people)?
Whenever possible I'd create from nearest similar vanilla creature (or rather vanilla + BG2Fixpack). Specifically for people I'd advice to create a character ingame first, but you already know that.
2. How do ability modifiers get applied and how are they displayed in the NI.
NI shows base numbers before modifiers from characteristics are applied. That's 100% true for AC/Dex and for HP/Con. I was unable to come up with a simple enough test for THAC0 because I'm not sure how to check for base THAC0 ingame (whether the amount displayed in the character screen would be influenced by being a fighter with zero stars in unarmed), but I fully expect it would generally work in the same way.
Note though, that there's two fields for AC in cre file: to my tests only "effective AC" affect creature ingame, setting its base AC (counter-intuitive, I know).
3. Effects: is there are some tutorial about effects?
Sadly, no, I miss one dearly myself, especially in regard of targets/durations. For example I was unable so far to create an item with "while equipped" effect where the effect itself is provided through opcode 146 "cast spell". There's a trick to learn a bit on your own through observation: in NI open any effect, change the actual effect field to the effect you're interested in, and do a search for selected attribute. This will give you all instances where this effect were used, and you'll be able to learn what settings were set to attain this or that implementation of effect in question.
4. I created kensai lvl 12 and converted it to created to .CRE. When I open it I see a whole bunch of effects that (as I understand) emulate kit bonuses: x4 increase THAC0 (278), x4 increase damage(73), x4 increase speed factor(190). But there are some very confusing moments:
a) Why each THAC0 and damage effect increases corresponding stat by 1 ('value' field) but speed factor increases incrementally 1,2,3,4 ('amount' field)?
b) It's logical to assume that only last of the speed factor effect gets applied, but how is it implemented? As plausible explanation I discovered that only last of the effects has coordinates set to valid values but then why all of the THAC0 and damage effects works properly? I mean that both THAC0 and damage effect has coordinates set only in the last effect too so, consequently, I would expect to see +1 bonus in game and not + 4.
c) Some questions about "Target" field in effect structure. Specifically: when should I use "None (0)", why "Preset target (2)" is used for above effects and not "Self (1)" and what is "Self (1)" then.
d) Why MODIFYPROFICIENCY is "None (0)" and is it applied in runtime (its bonuses to THAC0, damage, etc)?
e) What is "Used internally" field?
a) & b) I've re-created kensai lvl12 chr -> cre, and for me amount in each case of opcode 190 set to 1. Also I only got 3 opcodes 190 which is correspondent with "for every 4 levels" description while you mention 4. Can it be that you did something wrong?
c) & d) I wish to knew that as well Experiments and testing is your best friends to get the desired effect, and dissecting other mods can help, but fundamental knowledge of targeting and duration options of effects would be of huge help if anyone care to write an essay on that Modify Proficiency is permanent, but the impact of that permanent effect is indeed applied runtime per wspecial.2da.
e) Huh? Can you elaborate?
5. Do I have to add all the memorization info (7 priest levels, 9 wizard, etc) even for non-casting creatures?
Of course not, why would you?
6. So in the end I need to create enemy kensai creature. Do I emulate kensai bonuses via effects or do I hardcode it into stats, if possible? Looking through game creatures I see that hardcoding is a go-for method but I still want to hear it from experienced people.
You can go either way, really, but creating kensai ingame and then turning it to cre is simpler in that you won't have to count how much of which bonus is appropriate for given level: the game will do it for you. Just don't forget to remove any protagonist innate abilities in case you originally created him in singleplayer or the 1st slot of multiplayer.
7. My Ray NPC is assassin so I based it upon Yoshimo creature file. When I studied yoshi10.cre I noticed that innate profession skills are not memorized but he still has them in the game. Why/How?
Engine provides these ingame: notice how when you join Yoshimo the engine says "Yoshimo - Special Snare: Yoshimo". That's because before that, as a creature, he didn't have those, which is consistent with your observation. See here to learn which abilities are applied and how, and you'll know what you had to apply/recreate for your creature.Sorry I forgot you're making an NPC, not an enemy creature. You won't be needing that for an NPC, the game will sort it itself.