This question can be decided on two bases; Grammatical/Semantic and Narrative flow.
The operative word he in Gen 3:9 is the final word in the verse, אַיֶּֽכָּה - the interrogative adverb being אַי = "Where" which occurs 36 times in the OT (eg, Gen 3:9, 4:9, 16:8, Deut 32:37, Judges 13:6, 1 Sam 9:18, etc) and is almost always correctly translated as "where".
All versions that I could find translate as "where" (I could find no exceptions in Gen 3:9). The BDB meaning is given below in the appendix and lists the meaning as "where?".
Note that the story in Gen 3 contains the following elements:
- Adam and eve sin by eating the fruit (V1-6)
- They sew fig leaves together to hide their bodies (V7)
- God comes to talk and they hid (V8)
- God calls, "Where are you" (v9)
- Adam replies that he was naked and afraid so he had hidden himself (V10)
Thus, the flow of the story demands that God ask "Where?" rather than "How".
APPENDIX - BDB meaning for אַי
- interrogative adverb where?
a. so with suffix אַיֶּ֫כָּה [a verbal form, see Sta§ 355 b. 3]
Genesis 3:9; אַיּוֺ Exodus 2:20, poetry where is he? = he is nowhere
Job 14:10; Job 20:7 (Jeremiah 37:19 read Qr אַיֵּה); אַיָּם Nahum 3:17
(in indirect question) and the place thereof is not known, אַיָּם
where they are. Idiomatically, with the suffix anticipating the noun
to which it refers (Ew§ 309 c, compare DrSm. i. 21, 14) 2 Kings 19:13
אַיּוֺ מֶלֶחחֲֿמָת where is he, the king of Hamath? ("" Isaiah 37:13
אַיֵּה) Isaiah 19:12; Micah 7:10. When used alone, or with other
adverbs (see below), it is contracted to אֵי Genesis 4:9; Deuteronomy
32:37; 1 Samuel 26:16; Proverbs 31:4 Qr. (The more usual form is
b. strengthened by the enclitic זֶה (see זֶה, 4 אֵיזֶֿה15 where, then
? (never of a person, except Esther 7:5 (late), & only once 1 Kings
22:24 [but see 2 Chronicles 18:23] with a verb) Isaiah 50:1; Isaiah
66:1 (twice in verse); Jeremiah 6:16, in indirect question 1 Samuel
9:18; in the phrase אֵיזֶֿה הַדֶּרֶח ֗֗֗ where is the way (that) . . .
? 1 Kings 13:12; 2 Kings 3:8; 2Chronicles 18:23; Job 38:19 a. 24.
2 prefixed to other adverbs or pron., אֵי imparts to them an
interrogative force: thus
a. אֵיזֶֿה which (of two or more)? only Ecclesiastes 2:3; Ecclesiastes
11:6 (late), in indirect question
b. אֵימִֿזֶּה whence ? (מִזֶּה = hence; see below זֶה) Genesis 16:8
אֵימִֿזֶּה בָאתְ 1 Samuel 30:13; 2 Samuel 1:3,13; Job 2:2; in indirect
question Judges 13:6; 1 Samuel 25:11; with substantive annexed 2
Samuel 15:2 אֵימִֿזֶּה עִיר אַתָּה literally whence, as regards city,
art thou ? Jonah 1:8.
c. אֵילָֿזֹאת Jeremiah 5:7 upon what ground ? (ᵑ9 super quo? how? With
other adverbs, אֵי coalesces into one word, see אֵיכָה, אֵיכָכָה,