As a matter of good data hygiene, I've moved my home folder unofficially to a second drive and click-dragged folders into the left MyComputer panel.

On a fresh boot, those folders have an orange exclamation mark on them. If I click, I get a "Could not find [location] error."

When I click on the drive in Nemo (Under My Devices), the exclamation points clear and the shortcuts are accessible.

I don't think it's JUST Nemo, because Asunder also can't find a folder (and it annoyingly reassigns the folder when it does).

The drive is set to automount at startup and be visible in UI with no additional authorization.

May be of interest:

schipelblort@schipelblort-MS-7C02:~/Desktop$ cat fstab
cat: fstab: No such file or directory
schipelblort@schipelblort-MS-7C02:~/Desktop$ cat /etc/fstab
# /etc/fstab: static file system information.
#
# Use 'blkid' to print the universally unique identifier for a
# device; this may be used with UUID= as a more robust way to name devices
# that works even if disks are added and removed. See fstab(5).
#
# <file system> <mount point>   <type>  <options>       <dump>  <pass>
# / was on /dev/nvme0n1p3 during installation
UUID=a2cc79fc-e10e-45a9-b33d-f88b8e8f5b56 /               ext4    errors=remount-ro 0       1
# /boot/efi was on /dev/nvme0n1p2 during installation
UUID=F960-1EE4  /boot/efi       vfat    umask=0077      0       1
/swapfile                                 none            swap    sw              0       0
/dev/disk/by-uuid/4a7c4523-15a1-4552-b696-c0f510d57184 /mnt/4a7c4523-15a1-4552-b696-c0f510d57184 auto nosuid,nodev,nofail,x-gvfs-show 0 0
schipelblort@schipelblort-MS-7C02:~/Desktop$ lsblk
NAME        MAJ:MIN RM   SIZE RO TYPE MOUNTPOINTS
sda           8:0    0   3.6T  0 disk 
└─sda1        8:1    0   3.6T  0 part /mnt/4a7c4523-15a1-4552-b696-c0f510d57184
sr0          11:0    1  1024M  0 rom  
nvme0n1     259:0    0 953.9G  0 disk 
├─nvme0n1p1 259:1    0     1M  0 part 
├─nvme0n1p2 259:2    0   513M  0 part /boot/efi
└─nvme0n1p3 259:3    0 953.4G  0 part /
schipelblort@schipelblort-MS-7C02:~/Desktop$ sudo blkid
[sudo] password for schipelblort:          
/dev/nvme0n1p3: UUID="a2cc79fc-e10e-45a9-b33d-f88b8e8f5b56" BLOCK_SIZE="4096" TYPE="ext4" PARTUUID="c7b27e82-8a50-4d42-a90d-c9f8937a713b"
/dev/nvme0n1p2: UUID="F960-1EE4" BLOCK_SIZE="512" TYPE="vfat" PARTLABEL="EFI System Partition" PARTUUID="b1c74bb7-e22f-4dc6-9f2e-4d7350c1a42b"
/dev/sda1: LABEL="MyData" UUID="4a7c4523-15a1-4552-b696-c0f510d57184" BLOCK_SIZE="4096" TYPE="ext4" PARTLABEL="Basic data partition" PARTUUID="4448ba6e-63aa-4a08-a2de-32bcc50125a4"
/dev/nvme0n1p1: PARTUUID="5f108e85-c24a-4750-b0d9-0d9830e05281"

What does

cat ~/.config/user-dirs.dirs  

say?

alex@alex-MS-7C02:~/Desktop$ cat ~/.config/user-dirs.dirs  
# This file is written by xdg-user-dirs-update
# If you want to change or add directories, just edit the line you're
# interested in. All local changes will be retained on the next run.
# Format is XDG_xxx_DIR="$HOME/yyy", where yyy is a shell-escaped
# homedir-relative path, or XDG_xxx_DIR="/yyy", where /yyy is an
# absolute path. No other format is supported.
# 
XDG_DESKTOP_DIR="$HOME/Desktop"
XDG_DOWNLOAD_DIR="$HOME/Downloads"
XDG_TEMPLATES_DIR="$HOME/Templates"
XDG_PUBLICSHARE_DIR="$HOME/Public"
XDG_DOCUMENTS_DIR="$HOME/Documents"
XDG_MUSIC_DIR="$HOME/"
XDG_PICTURES_DIR="$HOME/Pictures"
XDG_VIDEOS_DIR="$HOME/Videos"

Ah, ok, I think what might be happening is because I just mirror the naming conventions of home on the second drive, maybe its getting confused?

So instead of going directory by directory, how can I just change the absolute location of home?

I would first change your mount point for the second drive so that it is mounted under

/media

and not

/mnt

Be sure to chown and chmod it accordingly.
This in itself will resolve the issue with nemo not accessing links to the second drive until you first access it manually.

Then, if you really want to have your home folders recognized where they truly are, modify the user-dirs.dirs file to reflect the absolute paths to your home folders and reboot.

As with any system modifications, first make a backup!

That's weird. When I dragged the folders over, they were mounted to /media. Hm. And it no longer worked to click on it since the folders were still pointing to /meda. Weird.

Well, everything is working now at least. I wonder if it's going to get pulled back to /mnt for some reason?

I don't know how that could happen aside from you unmounting it from /mnt and remounting it under /media. Your fstab is mounting it under /mnt at boot. Until you change the fstab, it will continue to be mounted under /mnt every time you reboot, and you will continue to have to access it manually before it is truly accessible to the system.
/mnt is a special mountpoint for temporary, manually mounted drives, not system drives or system partitions.

You don't have to use /media, but since other, removable media will be mounted there, I find it practical to keep everything together. Just create the mountpoint folder in advance and set the ownership and permissions (you have to do all that as root), and then fstab will happily mount it there once you change that entry as well.

I also don't think you should use

auto nosuid,nodev,nofail,x-gvfs-show 0 0  

in fstab, but you should instead be using

ext4 errors=remount-ro 0 2  

Keep in mind, if you mess up fstab, the computer will no longer boot. Be sure to check it before rebooting with:

sudo findmnt --verify  

Example fstab:

UUID=4a7c4523-15a1-4552-b696-c0f510d57184 /media/schipelblort/4a7c4523-15a1-4552-b696-c0f510d57184		ext4	errors=remount-ro 0 2  

Example mountpoint:

/media/schipelblort/4a7c4523-15a1-4552-b696-c0f510d57184  

It needs to be owned by schipelblort and the permissions can be standard 755 or 750.