ROYCH: This is partly guesswork, but I think it may explain why your problem occurs.
When OS X is controlling your computer (as it always does on a Mini), the file Type and Creator attributes that OS 9 uses to identify different kinds of files are not used. OS X ignores them in files that have them. Files that are only used by OS X don't have them at all. When you create a new application in Classic mode under OS X, those attributes may not be assigned to it, so the new application may not have any.
But if you copy the new application to a computer running OS 9, and those attributes are missing, the OS 9 computer will have no idea what sort of file it is. OS 9 won't even know it's an application. To prevent that, I'm guessing that OS X somehow builds clues into the file that enable OS 9 to identify it as an application, and to give it the Type attribute APPL. I believe any file in OS 9 that has that Type attribute will display the Memory menu item in its Get Info window — not only in OS 9, but in OS X. So after you copy your compiled application onto a computer running OS 9 and then back onto your Mini, it has the APPL attribute, and the Memory item is available in its Get Info box.
I have one application,
File Buddy, that can (among many other abilities) display and edit the OS 9 Type and Creator attributes of any file while running in OS X. It can be used to assign specific Type and Creator attributes to a file that has none. You could use it to assign the appropriate Type and Creator attributes to your compiled applications while you are running OS X. After you do so,
maybe they will display the Memory menu item in their OS X Get Info boxes.
If this works, File Buddy can apply the same changes in Type and Creator to a whole folder full of files at once. That would be an easy way for you to accomplish the same thing for several compiled applications instantly, without having to copy them to a computer running OS 9.
I don't create applications, so I can't test this procedure to see whether it works. I will be interested to hear what happens if you experiment with File Buddy.
But after saying all this, I really have no idea whether the message you're seeing about insufficient memory is meaningful or spurious. You may go through the whole rigmarole of changing the memory allocation for your compiled applications, only to find that doing so still doesn't enable you to open them. I'll be interested to hear whether that's true, too. Good luck.