Running python from AppleScript

This is a common finding - the shell environment invoked via do shell script is not the same as that you see in Terminal.app (specifically, it doesn't invoke any shell init scripts that setup paths; your working directory may be different; access controls are a little different; etc.)

In this case, though, since you're just invoking python with the path of the script, it sounds like the problem is the current working directory, which the script doesn't have access to. The simplest way to fix this is to include a cd command in your shell command string:

do shell script "cd ~/Desktop/; python3 /Users/me/Desktop/Folder/my_python.py" 

Now the shell script will set the current working directory to your desktop (or wherever you specify) before invoking the script.

Using Python3 in an AppleScript handler to toggle grayscale on Ventura 13.1:

# reference: https://indiestack.com/2019/04/toggle-system-grayscale-mode/
# tested: macOS 13.1, Python 3.9.6, 3.11.1
use scripting additions

my toggleGrayScale()
return

on toggleGrayScale()
	# use python3 from Apple command line developer tools for Xcode
	# but also works with Python 3 (e.g. 3.11.1) from Python.org
	return (do shell script "/usr/bin/env python3 <<-EOF - " & "

from ctypes import cdll

lib = cdll.LoadLibrary(\"/System/Library/PrivateFrameworks/UniversalAccess.framework/UniversalAccess\")
lib.UAGrayscaleSetEnabled(lib.UAGrayscaleIsEnabled() == 0)
EOF")
end toggleGrayScale

The caveat of using a Python handler in AppleScript is that you must escape double quotes in the python code with \" and backslashes with \\.