Why those holes near beaches or shores occur? Is there a setting to disable them if they are a feature?

Out of curiosity, what's your terrain_scale value set to?

It's set to 0.3

Here's my whole config:

{
"experimental": {
"horizontal_mountain_scale": 0.05,
"increased_height": true,
"terrain_scale": 0.3
},
"features": {
"deeper_oceans": true,
"desert_dunes": true,
"lava_rivers": true,
"snow_start_offset": 128,
"underground_rivers": false
},
"legacy": {
"enabled": false
},
"mod_enabled": true
}

Out of curiosity, what's your terrain_scale value set to?