No, you won't get into trouble for ignoring orders. All they are is worth some renown for completing them, so if you don't think you can do it, then skip it and go hunting. The fleet boats will have problems sneaking into harbors just because of their size; they are in roughly the same size category as the Type IX boats from SH3. Even the Tambor and Gar are 1400+ tons and have periscope depths of 60 ft.
I did the Osaka photo recon tonight, and it turned out to be a nail biter. Once again the weather got me into trouble. The approach was easy, too easy in fact. Most of the trip from Midway was done at Ahead 1/3. I'd submerge about 30 minutes before dawn and surface again about 30 minutes after dusk, and avoided all air contacts that way. When I got down to the narrows I waited for dark before going in, and went in on the surface. Well, it was storming so I couldn't see what the defenses were, but I made it in without a contact. I sailed up into the deeper pool in the middle of the bay, came to a halt, and waited the day out. In the early afternoon, I moved on up to where it started getting shallow again; I ran at 32x TC while looking through the observation scope to see mines, but didn't encounter any.
I eventually stopped here and watched for a while. I used the sonar tracks to plot out the courses a few merchants were taking, so I was certain is was mine-free.
That's when I went on in, and discovered the problem. It was still raining, and I couldn't see jack! I kept creeping closer and closer, and still couldn't see anything. I could make out ship silhouetes against the horizon in a couple of places, but nothing that could be identified or photographed. Eventually I plotted out where I thought ships were by those silhouetes. The water was so shallow I had to come up to 40 feet depth.
I wound up sailing all the way into the harbor, had to get within about 600 feet of a ship just to be able to see it, and photographing it was right out! Apologies for the darkness of this one.
So, I went back out to my LP/OP and waited another day. The following evening the weather had cleared, so I went on back in and found some juicy ships to photograph. Apparently Osaka is a big merchant port, because there weren't any major warships there.
So, I beat feet back out into the deeper area. Here's where things went horribly wrong. I was waiting out the day under time compression when I get hordes of sonar contacts; apparently a convoy was coming in. I tracked them, but they weren't going near me. Well, I left time compression on and went to the bathroom, which was a big mistake. The convoy changed course and sailed right over me. Now, I was motionless, about 110 feet down (10 feet or so above the bottom, any closer would cap time compression at 4x) and rigged for silent running. Somehow they detected me and started dropping depth charges. When I heard explosions going off I had to run back in from the toilet!
Well, I reloaded the save game at that point (after finishing the call of nature) and avoided the convoy this time, but unfortunately now with the clear weather I had to avoid the defenses I blindly sailed past on the way in. There was a subchaser sailing back and forth in the shallows, a medium gunboat, plus a few shore batteries. I had fun slipping back out. I couldn't do it unseen; one of the shore batteries opened up on me but I didn't get hit and eventually made it out. Whew! I don't think I'll be going here again.