how to conjugate verb in dependent clause inside subjunctive mood

None of those sound right to me. I would write:

I pretended that I understood, lest he think me stupid or deaf.

Reference

I think if you studied clauses with lest in literature you would find all three possibilities. Even "should" can be used.

"I were" is the correct subjunctive form here. However, "lest + subjunctive" marks the sentence as an archaic construction. Even "lest he think me", which is probably better, is subjunctive and feels old-fashioned.

If that's not what you intend, various modern alternatives are possible. How about, "I pretended that I understood, so he would not think I was stupid or deaf."