This is too trivial for Kanji Nut. I’ll put it here for now.
At one stage 堀 and 掘 were interchangeable but in the end 堀 came to refer to the noun and 掘 to the activity (Henshall 1824). That’s rather vague. When did this happen, and who made it happen? Unclear. But of course Hanshall makes vague statements like that all the time (sometimes he indicates ‘the scribes’ as agent).
Classical Chinese has 堀 for a word (modern Mandarin kū) meaning: (1) cavern, grotto; den (also written 窟) (2) scoop up or out.
掘 pointed to a different word (modern Mandarin jué): (1) dig out, hollow out, gouge, scoop out; the physical act that creates a 缺, gap. (a) excavate, unearth, dig up. (b) indentation, hollow, recession. (2) use up, exhaust; devoid of, deplete(d). (3) rise up sharply, protrude (also written with 崛). However, apparently in ancient times 掘 was also used to write that earlier word (modern Mandarin kū) for its meaning of ‘cavern’ etc. (which then could be written 堀, 堀, or 窟 - this all according to Kroll). In any case, Schuessler thinks that this one word kū and the other word jué, while pronounced somewhat differently in ancient times as well, were definitely related. In Japanese Sino-Japanese all of this (including 崛) is simply kutsu.
Schuessler’s old Chinese has ‘dig in the ground, underground’ 堀; ‘cave; hole’ 窟 (and 掘 ‘dig out, dig through [earth]’) (p. 337). Modern Mandarin seems to have 窟/堀 kū for ‘hole; cave; den’ and 掘 jué for to ‘dig’ (DeFrancis; Cedict; Lin Yutang).
In conclusion, both modern Mandarin and Japanese reserve 掘 for the activity of digging. In modern Mandarin a clearly different word for ‘hole; cave; den’ is preferentially written 窟.
※ 洞窟（どうくつ）1. [n,adj-no] cavern; cave; cave system; grotto (Modern Mandarin dòngkū)
Let’s look at Leonardo Boiko’s frequency list:
6574 ※ 洞窟（どうくつ） 1. [n,adj-no] cavern; cave; cave system; grotto 27616 ※ 岩屋；石屋；窟（いわや） 1. [n] cavern; grotto 35027 石窟 （せっくつ） (n) cavern; grotto; rock cave 42784 窟土 - 47644 栄窟 - 51982 岩窟；巌窟（がんくつ） 1. [n] cave; cavern 109578 仙窟（せんくつ） 1. [n] enchanted cave 109977 魔窟（まくつ） 1. [n] den of thieves 2. brothel; red-light district 3. [col] cluttered room 122631 貧民窟（ひんみんくつ） 1. [n] slums 173550 窟古 - 176152 私娼窟 【ししょうくつ】 (n) (arch) brothel; house of ill repute; red-light district; 184664 窟神 - 201834 窟咄 - 242804 窟院 - 265842 窟渓 - ... 308991 阿片窟；鴉片窟（あへんくつ） 1. [n] opium den ...
