I don't see a p-trap under there either.
Mortar can be wet above the vinyl liner that is clamped into the shower drain.
I have a very slow leak in the shower pan of a tile shower. I noticed a very slight water spot on the ceiling below the shower and when I pushed on it the drywall broke. Here are some pictures of the nice stalactite that has formed over the years. The shower is 28 years old and I really do not want to have to re-do the complete shower myself, I would have to hire a tile person for that. But, I think I could handle removing the tile to a certain height and just replace the bed. The tile is just white, the new would probably look different but at this point I do not care.
I also noticed that the mortar has filled the weep holes in the drain, and it seems to be draining as it is always wet. I have not showered in three days and it still is dripping every so often from the stalactite. About three drops a day, so I guess the mortar is saturated with water and will drip for a while. From the pictures there is no leak at the drain. I am concerned about no trap here, it must be on the other side of the joist, as I do see water down in the 90 degree. Never had a sewer gas problem. I see no leak in the water supply to the shower and opening up the shower faucet, everything back in there is bone dry. And no water coming down the supply pipes going up threw the floor.
So, re-tile the whole thing or try a patch job?
If the liner is flat on the floor, rather than on a presloped bed as is required by codes (but some places seem to ignore that), the mortar can and will be wet. Unless you find there's a leak in the actual piping, the only real way to resolve this is to tear things out to about 12" above the pan and redo it. But, most people decide if they're going to tear that much out, it not much different to tear the whole thing out, update the plumbing and valve, and rebuild to current standards. The liner needs to go at least 3" above the top of the curb, then you need to deal with the liner and the vapor barrier in the walls.
Important note - I'm not a pro
Retired Defense Industry Engineer; Schluter 2.5-day Workshop Completed 2013
Looks to me to be a complete do over. I studied your pictures and you have a few issues here.
1). Home made PTrap
2). Compromised floor joists (no drilling with in 2" of the top or bottom)
3). Your repair is not working. Looking at the pictures it appears this shower has already been "Fixed"
Why not rip out the shower pan and wall tile 12"-18" up. Find a new white tile and go again. If you can afford brand new then go for it.
How about a nice barrier free shower next time?