Sometimes, if we have a lot of SSH keys in our ~/.ssh directory
No, that's not how it's supposed to work. Ideally, one key per machine per user.
No, that's not how it's supposed to work. Ideally, one key per machine per user.
It doesn't really matter how many you have, you still need to protect them. Encrypt your laptop, lock your screen when you get up for a break, etc, etc.
Use IdentityFile to specify which key to use with which remote host and you're golden.
edit: I also have that private SSH key on my personal computers so I can use SSH when working from home. Then when I stop working with that company I can simply remove that key, rather than generating a new SSH key and redistributing public keys to hosts that I use regularly.
edit edit: Using IdentityFile also helps automate the process of redistributing keys when you decide to generate a new one.