I also concur, ENC does not always show for me.
It is also normal that you may be hearing P25 in the clear on the same channel. More than likely some mobiles are not transmitting with encryption.
What I've found on the 396 or 996XT's is that if you are in Scan or Search mode, the scanner will often not show ENC. It will usually just skip right past the channel and keep on scanning. If you are sitting on a channel that had some in the clear chatter while in the Scan or Search mode and a user comes on that is encrypted, I do see it light up ENC for a very brief time before moving on.
If you Hold on the channel or talkgroup in a trunked system, then mine have always shown ENC when an encrypted user is talking but again, I must be held or holding on that channel in a conventional system or holding on a talkgroup in a trunked system. If I'm scanning or searching either type of system, ENC usually never displays as the radio knows to keep scanning or searching so it never has a chance to display ENC.
Sometimes during a scan or search, if you are using remote software such as Pro96com or any of the others that allow remote operation, you can catch it display ENC but only in the software display as it is slower than the radios display. ENC may also not display at all if older forms of encryption are being used. Usually the radios will also stop on those types of encrypted channels though.
I should also add that I monitor the STL City P25 system here in Missouri. They don't have any fully encrypted TG's but do have several users that use encrypted radios. When monitoring that system with a Uniden, the Uniden never stops or anything when one of the encrypted users is talking. The only way I can tell is to turn on a GRE 500 or 600 and actually hear the encryption sound or place a Uniden into Hold mode on the talkgroup that the encrypted user is on. On the GRE, you hear the horrible sound of encryption while on the Uniden's, all you see is the word ENC on the held display but no audio is passed to the speaker. The GRE PSR800 is an exception to the rule. That model can be set to pure silence or a tone of your choice when it encounters encryption or you can make it pass the encrypted audio to the speaker just as the 500 and 600 do. The only drawback to that method is the PSR800 will stay on that channel or talkgroup until the signal has dropped where the Uniden's will continue scanning for in the clear talk instead of tying up the radio on an encrypted signal or channel. I don't recall how they do it on the Home Patrol but I think it simply skips encrypted audio much like the 396 or 996 do but without any screen indication that a signal is encrypted.
I own an HP1 so I guess I should try the hold mode and see what it says when encryption comes on the air.
On both models, you can tune the control channel and use Pro96com and it will indicate if a talkgroup is encrypted or not regardless if the audio is pumped to the speaker. It will display (Enc) in realtime when it detects an encrypted signal.
I'd guess that Unitrunker can also display that info but I don't use Unitrunker that often so I'm not sure.
edit: The HP1 does not seem to indicate it is hearing an encrypted signal even when held on a talkgroup.
It just mutes the audio when held or keeps on scanning when encryption is detected. I also did not see it indicate the RID when it was held on a TG with encrypted audio. It would only display the RID when it was an in the clear transmission.