Hmm, ok. I'm going to do this from memory mostly, but let's see(and by order, because that's the easist to go by):
In the original animed series they only had a few instances of "hiding"(mostly "Hey, someone left a blue mini-cassette player lying around!), or for comic relief(when Ironhide thought he found Red Alert in "Auto Beserk").
In Beast Wars, yeah, they honestly didn't even try to focus on any kind of disguise aspect. They had at least one bit of mistaken identity(Snowstalker), but otherwise ditto. Fortuneately I don't think the tagline was "Robots in Disguise" at the time. Same goes for Beast Machines.
Then we come to Rid. For a show that actually went back to the original tagline and vehicular Transformers, I don't remember them
ever trying to hide beyond the first episode, in which it was explained they'd been hiding the whole time. I haven't seen every episode, but from what I recall neither the bots or the cons tried to conceal themselves. Plus, how could a giant cyborg singing shark hide anyway

.
In Armada/Cybertron, there's actually a whole lot of hiding going on, particularly in Cybertron. In both shows each side tries to keep themselves concealed(the Autobots moreso of course) for as long as possible. It's never focused on of course, more of a sub-plot/aspect of the show, but it's certainly there. Energon as I recall had no disguise aspect.
Now onto the comics. Been a long time since I read the early Marvels, they eventually phased out the disguise part, not much of a factor there. Dreamwave never attempted to do the disguise thing either(save for when Sky Lynx was introduced, which was awsome).
Finally, we come to IDW comics. Disguise is a VERY important aspect in the Infiltration/Escalation saga, and really kicks the robots in disguise idea up a notch.
*Edit* Geez, I used the word "aspect" a lot!