Lara has got good enough intel on his wards to know that if Harry goes into lockdown as per DM he won't be able to get out again and therefore he would be the only option for Thomas to feed on. That does not read to me like they're a perfect defence against deducing information from/through.
So ... something he's done before? The wards aren't invisible to people with the Sight, nor is there any effort made to conceal them. The wards are on the exterior. They can be visually examined, ala the wards on the Corpsetaker's hideout in Ghost Story. The lab with Little Chicago is buried behind them, and depending on what how one views the efficacy of the circle around Lasciel's Coin ... right next to a Denarian Coin. I'm not certain one could look from the outside without disturbing the wards/Bob.
While, strictly speaking, true ... that's also a timespan when both Thomas and Murphy would have been noticed as missing.
IIRC, we have Harry's lunch with Lily and Maeve, several hours of stuff at the hotel with Murphy around at the beginning of it, Harry getting knocked out and captured by Madrigal, and then Thomas appearing to save the day. Depending on how long Harry is unconscious and captive, that's a span of a good few hours with Murphy unaccounted for and longer for Thomas.
For the lunch with Lily and Maeve, Bob is still in the lab.
Murphy was in charge of things at the hotel while Harry and Rawlins were captive - that was during the aftermath of the Xenomorph-phage attack.
Harry was unconscious for between an hour and an hour and a half. Thomas found Harry and Rawlins by following Mouse, and then was trying to figure out how to get inside and get Dresden and Rawlins out, sans new bullet holes.
Bob sees the change and deduces what it will do in moments.
Also, if you believe as I do that Cowl in WN is pulling his punches to not kill Harry while looking like he barely missed killing Harry, that entails deducing a fair bit about Little Chicago's capacities in a matter of a few seconds.
Little Chicago is a major undertaking in a direction of magic that Harry's really not focused on before. I think it taking him six months is comparable to Molly's slow progress with shields, frex. I can believe a Senior Council level talent like Cowl with some experience in that form of magic being able to figure it out and fix it on a scale of hours. I can believe an entity at Mab levels of superhuman being able to do it in minutes. (The analogy that seems apt here is that I have been doing a particular subset of computer-programming-type things professionally for close on twenty-five years, and there have been times in my particular field of expertise when I've been presented with a specific unfamiliar-to-me problem using basic principles I know well, and have solved or made more progress on it in ten minutes than people without that have been able to in months.)
Bob saw the change and what it did ... because he'd been involved at every stage of planning, prep work, and construction with Harry.
Combat power and non-combat ability to study complicated magical constructs are two very different things. Remember, Ancient Mai is good at the non-combat things, but isn't that good at combat (relatively speaking, of course). Wizard's have different talent areas. Thaumaturgy is an area that Harry is naturally good at - he's got a knack for it. Sure, Cowl (for example) would probably be able to figure out
what Little Chicago was in a short period of time - a magical construct representing a chunk of Chicago ... but that's a far cry from being able to figure out how Harry put it together or figuring out that it's got a lethal flaw, much less how to fix it.
According to Bob, Dresden has a gift for the kind of work involved with Little Chicago - and that none of the evil genius's Bob had ever worked for could have managed it, and most of the psychotics wouldn't have been able to either.
The Lea/Mab theory also has the side benefit of the fact that Lea (per her own words) had been following Dresden through the NeverNever, watching over him, even whilst he slept. Mab would have needed to do some of that, though she might have been able to delegate some of the watching, but she'd've been getting reports, and Dresden building Little Chicago is probably something that would probably draw some interest, something that she'd probably follow more closely, partly to see how Dresden was working it/progression of his skills, and partly because it's something that if it went wrong would definitely be something that wouldn't be good for Harry's well being.
As for it taking 6 months ... it's not because he's not good at it, it's because it's such a complex piece of work. Per Bob, Dresden's got a gift for this kind of thing - and that none of the evil geniuses he'd worked for could manage something like Little Chicago, and the same for most of the psychotics.
6 months of pouring energy into it, possibly another few months of design work.
Little Chicago is a highly detailed scale thaumaturgical duplicate of Chicago in a 2 mile radius from Burnham Harbor. That's not something that's going to be quick. Not if you want to build it with the necessary degree of accuracy.