Ok, let's assume you followed the guide to a T and you've got unlaunch + hiya, and are trying to get dsiware by copying the files and folders into the titles folder.
Folder structure should look like this:
└ [title id low]
| └ xxxxxxxx.app
| └ title.tmd
If you don't have that, or the files are invalid, then it won't show up on DSi home menu.
Alternatively, if you have everything right, and yet they don't show up on home menu, something that can happen is that Hiya may be silently failing to load, with Unlaunch falling back onto unlaunch/nand home menu, where your DSiWare obviously aren't installed. You can tell by the absence of sounds on the home menu. This can happen if there was something wrong with your nand dump when you used Hiya CFW Helper, you can fix it by making a new nand backup through fwtool, making sure it's not corrupted, and running Hiya CFW Helper on that new dump (it should automatically replace the unlaunch tmd from the new dump with a clean one, so you don't have to worry about that.)
In my case, it was caused by my nand backup having unlaunch tmd instead of the clean launcher tmd, because apparently the nand backup I made initially got corrupted, and Hiya would give me a black error screen on boot. So I had to make a new backup, but Hiya CFW Helper didn't replace the launcher tmd with a clean one (or maybe it was supposed to, but didn't, for whatever reason.) Newer versions of Hiya CFW Helper do automatically replace unlaunch tmd with a clean one, so this particular issue should not happen to anyone, but it's possible that something else is wrong with the contents of your SD, which could be making Hiya silently fail to load, and you'd be thinking that everything started up fine because you end up on home menu, without realizing that this is the wrong home menu.
Also, current release of Hiya CFW Helper has a bug, use the previous one (3.5), this is not necessarily related to your problem but it would be good to avoid further problems.