[Nexus 5X General] PiousInquisitor:
The updater script doesn't issue any command that explicitly deletes any files. Files are only replaced. However, the OTA may contain and replace ALL system files. Here are the relevant parts of the N OTA updater script:

show_progress(0.650000, 0);
ui_print("Patching system image unconditionally...");
block_image_update("/dev/block/platform/soc.0/f9824900.sdhci/by-name/system", package_extract_file("system.transfer.list"), "system.new.dat", "system.patch.dat") ||
abort("E1001: Failed to update system image.");
show_progress(0.100000, 0);

HERE is a thread that explains what the system transfer list and .dat files are.

You could test and see if all files are being replaced by fastboot flashing DP1, OTA updating to N final (with the full OTA) then checking to see if and night mode is available once you are booted up.

EDIT: someone has already done it.

http://xdaforums.com/showthread.php?p=68397093

The full OTA must include all system files. The people that have the night mode tile and any other leftover stuff must have taken normal OTAs. Those are delta updates that only update what has changed.

Here is the whole updater script for your viewing pleasure:

(!less_than_int(1469149941, getprop("ro.build.date.utc"))) || abort("E3003: Can't install this package (Fri Jul 22 01:12:21 UTC 2016) over newer build (" + getprop("ro.build.date") + ").");
getprop("ro.product.device") == "bullhead" || abort("E3004: This package is for \"bullhead\" devices; this is a \"" + getprop("ro.product.device") + "\".");
ui_print("Target: google/bullhead/bullhead:7.0/NRD90M/3085278:user/release-keys");
show_progress(0.650000, 0);
ui_print("Patching system image unconditionally...");
block_image_update("/dev/block/platform/soc.0/f9824900.sdhci/by-name/system", package_extract_file("system.transfer.list"), "system.new.dat", "system.patch.dat") ||
abort("E1001: Failed to update system image.");
show_progress(0.100000, 0);
ui_print("Patching vendor image unconditionally...");
block_image_update("/dev/block/platform/soc.0/f9824900.sdhci/by-name/vendor", package_extract_file("vendor.transfer.list"), "vendor.new.dat", "vendor.patch.dat") ||
abort("E2001: Failed to update vendor image.");
show_progress(0.050000, 5);
package_extract_file("boot.img", "/dev/block/platform/soc.0/f9824900.sdhci/by-name/boot");
show_progress(0.200000, 10);
ui_print("Writing bootloader...");
package_extract_file("bootloader-flag.txt", "/dev/block/platform/soc.0/f9824900.sdhci/by-name/misc");
package_extract_file("bootloader.sbl1.img", "/dev/block/platform/soc.0/f9824900.sdhci/by-name/sbl1bak");
package_extract_file("bootloader.tz.img", "/dev/block/platform/soc.0/f9824900.sdhci/by-name/tzbak");
package_extract_file("bootloader.rpm.img", "/dev/block/platform/soc.0/f9824900.sdhci/by-name/rpmbak");
package_extract_file("bootloader.aboot.img", "/dev/block/platform/soc.0/f9824900.sdhci/by-name/abootbak");
package_extract_file("bootloader.pmic.img", "/dev/block/platform/soc.0/f9824900.sdhci/by-name/pmicbak");
package_extract_file("bootloader.hyp.img", "/dev/block/platform/soc.0/f9824900.sdhci/by-name/hypbak");
package_extract_file("bootloader.keymaster.img", "/dev/block/platform/soc.0/f9824900.sdhci/by-name/keymasterbak");
package_extract_file("bootloader.cmnlib.img", "/dev/block/platform/soc.0/f9824900.sdhci/by-name/cmnlibbak");
lge_bullhead_update_gpt();
package_extract_file("bootloader.sbl1.img", "/dev/block/platform/soc.0/f9824900.sdhci/by-name/sbl1");
package_extract_file("bootloader.tz.img", "/dev/block/platform/soc.0/f9824900.sdhci/by-name/tz");
package_extract_file("bootloader.rpm.img", "/dev/block/platform/soc.0/f9824900.sdhci/by-name/rpm");
package_extract_file("bootloader.aboot.img", "/dev/block/platform/soc.0/f9824900.sdhci/by-name/aboot");
package_extract_file("bootloader.pmic.img", "/dev/block/platform/soc.0/f9824900.sdhci/by-name/pmic");
package_extract_file("bootloader.hyp.img", "/dev/block/platform/soc.0/f9824900.sdhci/by-name/hyp");
package_extract_file("bootloader.keymaster.img", "/dev/block/platform/soc.0/f9824900.sdhci/by-name/keymaster");
package_extract_file("bootloader.cmnlib.img", "/dev/block/platform/soc.0/f9824900.sdhci/by-name/cmnlib");
lge_bullhead_recover_gpt();
package_extract_file("bootloader.sdi.img", "/dev/block/platform/soc.0/f9824900.sdhci/by-name/sdi");
package_extract_file("bootloader.imgdata.img", "/dev/block/platform/soc.0/f9824900.sdhci/by-name/imgdata");
package_extract_file("bootloader.sec.img", "/dev/block/platform/soc.0/f9824900.sdhci/by-name/sec");
package_extract_file("bootloader-flag-clear.txt", "/dev/block/platform/soc.0/f9824900.sdhci/by-name/misc");
ui_print("Writing radio...");
package_extract_file("radio.img", "/dev/block/platform/soc.0/f9824900.sdhci/by-name/modem");
set_progress(1.000000);