I originally posted about this in the thread for little questions because I thought it was just a low chance fluke. I had a merc secret base string of missions in Europe. I have all of Europe covered with a decoder. I didn't think I could handle any of the merc ships, so I just ignored them. Didn't try to intercept or land at any of the grounded ships, they were completely unopposed, but no base showed up. I thought there might be some kind of delay, like bases only spawn at the start of the month or something, so I kept playing. The same month the Academy had a secret base mission in the Pacific, and I got a few of their landed ships in Hawaii. 2 frigates and I think a cruiser (vanilla battleship map). No base for that one either. There are some islands near Australia that I don't have coverage on, so I don't know for sure that they didn't set up one there, but about half the ships that landed in Hawaii did get raided and defeated. Earlier in the campaign I did have an academy base show up in South Africa. I had no coverage in the area at the time and found out about it from the rumors popup.
I had taken a break from the game and just got back into it at the end of August. This campaign is a new one from that version (0.99j6). I haven't updated since that install. Unfortunately, I don't have a save from when it happened. I'm attaching the oldest one I have, which I think was a month or two after it happened. Not sure if that'll be helpful at all.
I haven't edited any of the rul files, and the only save game editing I've done was give myself some obsidian credit chips after I stupidly built a good chunk of a base without staffing anyone to defend it and it got wiped out. I can't remember for sure now, but that may have happened before the academy base in south africa.
I generally don't like updating mid-campaign, so I was planning to stick with this version for a while anyway. If I get any more secret base missions (especially ones that don't generate a base) I'll grab a save and post it here