Setting the value of a Numbers cell using AppleScript
I'm in front of a Mac again and gave your code a go and also got the same error, so it's probably somewhat misleading in terms of what it actually means.

However, I did play around with your script a bit and was able to get the code to work by using the following code:

tell application "Numbers"
  tell table 1 of sheet 3 of document 1
    set the value of cell 1 of column "E" to 1000
  end tell
end tell


However, now that I've got this to work, I just wanted to flag you seem to be hard coding the cell etc. That is, if the position changes then the script isn't going to be dynamic. Whether this is an issue for you or not will depend on what you're trying to do and how your Numbers spreadsheet is designed.