How do I get access to `/Applications` from the command line?

Starting in Catalina (10.15), macOS uses a split-volume format, with the system software on a locked volume and a separate "Data" volume for user data, user-installed software, etc. Most folders contain just one of these things, so they reside on just one volume, but the Applications folder has both, so it's handled... strangely.

What's really going on is that there are two Applications folders. The built-in system applications are in /System/Applications (which is on the read-only system volume), and user-installed apps (including Safari, 'cause it's weird) are in /Applications (which is actually a firmlink to /System/Volumes/Data/Applications on the Data volume).

Net result: at the command line, you have to look in two different places, /Applications and /System/Applications, to see all of the apps installed on your Mac.

The Finder shows their contents merged together, but this is just a convenient illusion -- the reality is that there are two different folders, and at the command line you see that reality.

Here are a couple of good articles at the Eclectic Light Company about this: "macOS Catalina Boot Volume Layout" and "Big Sur boot volume layout".

I am not sure why you want to enter the command below.

open /Applications/Messages.app

I believe the proper command would be the following.

open -a Messages

Basically, the operating system is separated into a read‑only volume and a read‑write volume. These volumes can appear separately or as combined. When using the Finder, you viewed as combined. From the Terminal, you accessed just the read‑write volume. So while the command below would work by accessing the read‑only volume, using the -a option would not require knowing where the application resides.

open /System/Applications/Messages.app