The Thieves Guild is much less powerful in Morrowind; they need the numbers, so why hide themselves? The Camonna Tong may just wipe them off of Morrowind itself.
That fact did not escape me, but that seems like a reason to be more selective, not less, If they were smart, they would hire only outlanders, and people who were known to actively attack the Camonna Tong, by actively attack, I mean go into bars controlled by the Camonna Tong, and kill everyone there. There would be background checks, and you would have to actively search for the TG in order to join. I was actually completely shocked that it never occured to the Camonna Tong to infiltrate the TG and eventually kill them that way...
The Thieves' Guild obviously has considerable power in Cyrodiil, so guards could be cracking down harder on them along with other implications, causing them to better conceal themselves.
It seemed more like the guards knew and were just trying to cover it up. My guess is the TG has the guards pretty much in control, In fact this seems strongly implied, Though if that is the case, then the whole thing about relocating Lex was just retarded, they could have done it simply through bribery, so now I'm confused again...
It's rather elementary to me: Morrowind's TG is weaker and desperate, Cyrod's is more prominent, and people have convenient [censored]-ticity and ignorance.
Considering their ability to remove any and all bounties from their members' heads, I'd say the Thieves Guild have the guards pretty much infiltrated, Thieves Guild members are probably undercover as guards, furthermore The higher-ups are bribed, if this is impossible, then they are restationed or fired, as Lex was, if this is not possible, they are blackmailed, if this is impossible then as a last resort they are murdered. Well maybe not murdered... The Cyrodiil TG seems like a bunch of Robin Hoods really, and don't want to actually kill anyone.