As native speakers, do you pay attention to add s/es or it comes naturally without thinking?

Naturally, 10000%, unless your home dialect is inconsistent about it.

Basically we add -es to words that are unpronounceable (or at least very difficult to pronounce) with simple -s. So it isn't merely out of practice, but out of necessity. \-s pronounced /z/: >trees, tubs, foods, hogs, sills, stems, stones, songs, doors, tithes, gloves \-s pronounced /s/: >books, laughs, stops, pots, mammoths \-es (pronounced /ɨz/): >finches, beiges, judges, sauces, flashes, roses These are all based on phonetics. It is very hard to say /z/ (or /s/) after another sibilant. And as to /z/ vs. /s/, it is very hard to say /z/ after a voiceless consonant.

It is very natural for native speakers. 

It comes naturally.

What s/es?

It's natural, and makes sense because an s/z sound followed immediately by another s/z sound is hard to pronounce.

I don't think about that. (Assuming you're talking about making things plural?)

It comes naturally without thinking.

Absolutely natural. It's part of the language, not some add-on feature you learn at a later time.

Your question is a bit unclear because there are different reasons to add -s to words. Are you talking about adding -s or -es to nouns to make them plural? Or are you talking about adding -s o -es to verbs for subject-verb agreement?

Learners at a decent level do it naturally as well.

Natural understanding as a native.