[Sprint HTC EVO 4G LTE] bigjustinturbo:
The issue with some apps not showing up is related to the file /system/customize/MNS/default.xml and inside, there is an entry that looks like this:

<function name="applications_hide">
<set name="plenty" max="7">
<item name="package">com.android.htcdialer</item>
<item name="class">com.android.htcdialer.Dialer</item>
</set>
<set name="plenty" max="7">
<item name="package">com.android.htccontacts</item>
<item name="class">com.android.htccontacts.ContactSearchEntryActivity</item>
</set>
<set name="plenty" max="7">
<item name="package">com.android.htccontacts</item>
<item name="class">com.android.htccontacts.ViewCallHistory</item>
</set>
<set name="plenty" max="7">
<item name="package">com.infraware.docmaster</item>
<item name="class">com.htc.FilePicker.FilePickerPolarisOffice</item>
</set>
<set name="plenty" max="7">
<item name="package">com.android.camera</item>
<item name="class">com.android.camera.MirrorEntry</item>
</set>
<set name="plenty" max="7">
<item name="package">com.melodis.midomiMusicIdentifier.freemium</item>
<item name="class">com.soundhound.android.appcommon.activity.SoundHound</item>
</set>
<set name="plenty" max="7">
<item name="package">tunein.player</item>
<item name="class">tunein.player.Activity</item>
<item name="flags">1</item>
</set>
<set name="plenty" max="7">
<item name="package">com.htc.htctwitter</item>
<item name="class">com.htc.htctwitter.TwidroidSplash</item>
</set>
<set name="plenty" max="7">
<item name="package">com.htc.friendstream</item>
<item name="class">com.htc.friendstream.SocialMainActivity</item>
</set>
<set name="plenty" max="7">
<item name="package">com.android.providers.downloads.ui</item>
<item name="class">com.android.providers.downloads.ui.DownloadList</item>
</set>
<set name="plenty" max="7">
<item name="package">com.adobe.flashplayer</item>
<item name="class">com.adobe.flashplayer.SettingsManager</item>
</set>
<set name="plenty" max="7">
<item name="package">com.htc.pdfviewer</item>
<item name="class">com.htc.pdfviewer.ActPDFReader</item>
</set>
<set name="plenty" max="7">
<item name="package">com.sprint.android.musicplus2033</item>
<item name="class">com.sprint.android.musicplus.MainActivity</item>
</set>
</function>

As you can see there's not just Tune In being hidden. There's Soundhound, a PDF Viewer which appears to be by Foxit based on the icon, Polaris Office, Downloads, Sprint Music Plus (whoopty fart), and a Mirror app which is actually part of the Camera app.

Editing out this section of the file, replacing the old with the new, and setting its permissions correctly (-rw-r--r-- / root:root) makes them appear in the app drawer. However, I haven't been able to test yet if this must be done before booting for the very first time (like after a wipe/flash for instance.)

I'm not sure what other ROMs are doing with this file, but flex360 has incorporated it into his bundle of mods: http://xdaforums.com/showthread.php?t=1701117

And if you use a replacement launcher like Nova or Go or whatever, you don't come across this problem at all. Everything is in your app drawer since they don't use this file.

One thing I can't figure out though is why even though there's a twidroid / Twitter entry in that file, and the stock install includes Twitter.apk, which I've confirmed is in my system/app directory, no Twitter app or widgets show up on my phone. It appears to integrated into Friendstream only. Interesting.

So yeah, no idea what was in their heads.