I think it makes a lot of sense that when a lot of things go missing when you're around would translate to distrust in the PCs.
Honestly, I think it should just have a negative effect, since the positive effect is the wealth increase.
Another way of doing it is also, like I suggested earlier, making it harder to do (say if you are caught sneaking around by an NPC they check your inventory for non-gold stuff you might've stolen, and take it back with a reputation hit on said NPC, etc.). This encourages spending ability/skill points on stealth abilities and lockpicking etc. in order to find ways around the NPCs and get in and out without bringing attention to oneself.
In general, either a more difficult system for thieving successfully, or an accruing reputation penalty (kind of like in Bethesda Fallout, negative karma per theft) for heavy theft.
What my entire goal is about, as many have probably seen elsewhere, is making choices appear to be choices of enjoyment or reward, not choices of practical superiority or gimping oneself. I think the increase in penalties/difficulty for thievery makes it an OPTION rather than a COMPULSION, which the extra wealth for time investment is simply tremendous at this point, and thus feels compulsory to do it.
Nothing should end up just being notably superior at completing and enjoying the game; every choice should be a choice of "I want to" rather than "I should (lest I suffer)" in the ideal enjoyable game experience though, I believe.
So here it would be preferable to have "I want to invest in thievery over combat skills so I can use the wealth for gear and extra skills etc (and because it is fun)" instead of "I should steal since it takes no real investment and significantly improves my combat odds, whereas not thieving does nothing for me practically (lest I suffer for being poorer than most characters and have more trouble needlessly)".
