EDIT : Okay i wrote a big "composition", if you don't have time, don't read even a word. Also don't start reading it from 2nd paragraph, because each paragraph is combined with the others.
I bet there is a professional way of crypting a cleo script. We could count some of FYP's crypted scripts as an example. But these crypters are kept like a secret. Why ? Because think about it from this point of view :
Imagine yourself as a guy who is scripting ÃBER 1337 PR0 HAXOR cleos, and you don't want unskilled, noob cleo scripters to see your pro code flow and way of scripting. They might even steal your codes, and rename and then sell them all over youtube as if they made it on their own, so ye, you can crypt them. But sometimes, somebody wants an easy script from you, and intentionally you don't crypt it, and sometimes, you give even it's source code in a .txt format. Why ? Because that guy will learn how to make it. And in the future, he will make cleos for himself too. And then he will teach others how to make it too. So that cleo scripting will not disappear by time. If you crypt even easy scripts, then nobody will learn anything. And when you leave samp, cleo will be already gone, because not much people will know about it. And their cleo knowledge will not be high enough to have fun with, they will be able to make only a single player car spawner, while they were hoping for a cleo mod that spawns samp cars all over the place and do tricks with them in a synchronized way. So they will find another scripting language, and cleo will be pushed aside just like an old toy on top of your bookshelf.
So, you are still that pro cleo scripter, and would you, in this case, still teach a cleo learner how to completely crypt the cleos ? If i were him, i wouldn't. That's why this is being kept as a secret. By the way there isn't a crypter software, but instead there are "ways" to crypt them. And luckily, not much people know about it, otherwise even i would learn no shit from easy and crypted scripts and then my cleo knowledge would never be high enough to make people use my mods. That's also why you can see the codes of drift.cs etc. To allow other guys to learn something and to get more experience.
I hope this was useful to read, useful for your uhh... ideas about crypting.