Timo said:
Quite possibly. Then again, it's currently good manners not to try and assassinate the real culprits even in times of war, but to only kill, hurt and maim their underlings and subjects of varying degrees of guilt. The explicit aim of coalition forces to assassinate Saddam in the two recent wars with him was somewhat out of line with established US doctrine and commitments in that respect.
Usually for reasons other than politeness, although I admit such concerns have shaped the manner in which a number of conflicts--in the West--turned out. The foremost example is of course Napoleon after Fountainbleu, upon whom the allies honored their agreements. However, a number of counterexamples come to mind, most immediately Yamamoto--a soldier, yes, but in essence a mover in the Imperial Japanese government. The concern over killing Soviet leaders (and their concern over killing ours) in any prospective nuclear war was born out of a need to have someone to negotiate with. This of course is somewhat discredited now, but before nukes became true world-enders (still an inflated description imo, civilization-ender is a better descriptor) graduated response was a feasible notion.
In the case of the Founders, the idea must have been to let them die and allow the Vorta to succeed to the command of the Dominion, in the hopes they could be negotiated with more successfully. Personally, I doubt this would have happened, although Weyoun (both standard-issue and defective) showed signs of apostasy in Treachery, Faith, and the Great River, and Keevan was practically an out-and-out traitor by Vorta standards.
OTOH, guilt of war could easily be extended to any number of underlings, subjects and bystanders, as was done in WWII where civilian populations were explicitly considered valid targets by the various parties - both in terms of "collective guilt" and in the concrete sense of each of them contributing to the war effort, however indirectly.
It would be difficult to assign such guilt to, say, the Jem'Hadar or the Vorta. The Founders on the other hand appear to all have had a part in the decisionmaking process, however superhuman and mysterious that process was.
A good question - but then again, in "Heart of Stone" Odo was in no way amazed that the Founder imitating Kira had in-depth information on DS9 events and happenstances. As in really in-depth, phrases spoken, holodeck mishaps suffered, the works.
We should assume that there were Founder agents on the station constantly at least from the second season on, doing extensive groundwork. Some probably remained till the very last, that is, the evacuation at the end of "Sacrifice of Angels". Whether they were shapeshifters or other operatives is unknown, but I'd be perfectly ready to believe in a Founder or five being present at all times.
Then a follow-up question: would mental scan techniques reveal the existence of a Changeling in place of a solid? Or would a Betazoid or Talosian or whoever be fooled by a potentially perfect copy--a biochemically, neurologically exact replica?
I tend to think the latter, given the recourse to telepathic techniques available to the Federation, Klingons, and Romulans, mind-melds, Betazoids, Medusans, mind-probes. Eventually, you'd think they'd just set up restraining devices like the one Tain gave Garak to work Odo with everywhere, but it's eminently possible and perhaps probable that it was only effective against Odo's poor stats.
Of course, this dictates that the true consciousness of the Founder exists somewhere else other than the physical form, but in a way we knew that already, since their mass is obviously inconstant as well (Odo the Bird flies but Odo the Dude can hurt you when he punches you in the face). I have a half-baked theory about how Founders are close to living transporter/replicator units with extremely low waste heat, but nothing concrete on this.
OTOH, Dr. Bashir might have been an ideal choice for abduction, as he was known to be somewhat detached from the community by his irritating mannerisms and sheer snobistry (both probably conscious choices, to better hide the dirty genetic engineering secret he harbored). Few people on the station probably had an inkling of what he did even when he was himself, professionally or privately speaking. And O'Brien had a good radar for such things in other episodes, but Bashir might have been too fluid a character for even the Chief to fully grasp.
You've got to wonder how bored the Changeling was shooting down Messerschmitts over the Channel.
The Dominion on multiple occasions did its damnedest to kill Odo, fir example by sending Jem'Hadar vessels to blow up a ship aboard which Odo was known to travel
In fairness, that ordinarily wasn't the Founders, it was the Vorta political officers or Jem'Hadar operational commanders, who may not have known or had reason to know Odo was aboard at any particular time, or, fearful of their masters, simply decided to avoid the question and do what seemed best at the moment. That would have been the typically Solid response, I'd wager.

At the least, the Dominion bureaucracy appeared to allow the Founders significant free time.
On a throwaway note, I wonder how far in the forefront of Ron Moore's mind the Founders were when he was creating BSG. Very similar theme, and very similar nitpicks.