First of all, pretty much all 1190 and 1290 exhausts are cross compatible with the 1090. Most cases, you can check the manf. website and it will come up with the same part number for all three...A good example is the yoshi exhaust.
Second of all, if you change the exhaust, its going to change how the motor runs. It may be fine, it may not. Depends on a lot of things. How the bikes tuned from factory, what type of exhaust, ect. ect ect. The problem with bikes now a days is they run so lean from factory to pass emissions that when you put an open exhaust on, your just making it worse and can run into some really lean conditions which can not only make your bike run like crap...but it could also cause predetonation that could in some cases damage the motor. HOWEVER, that is often times not the case. Like I said, it all depends.
Most people say stupid things like "oh, this pipe made me loose power on bottom.." or "These bikes like back pressure" Its all BS...The fact is, the less restriction you have on an exhaust, the more performance you will get out of it PROVIDED that you fuel it correctly. If you are just changing the muffler on your bike, which in most cases is what people do on motorcycles, you will probably be fine. But you will still be affecting the engine's performance if you don't change fueling along with it.
A lot of guys are opting for the rottweiler fuel dongles (basically just a resister plug) that replaces the stock narrowband O2 sensors. It tricks the bike into thinking the O2 sensors are at a certain reading, which will intern affect the fueling. It basically stops the bike from leaning out for emissions purposes (IE when they are trying to heat up the cat after first start, idling in traffic, ect) This will help to make the fueling less lean, but it wont "tune" the bike for your specific exhaust/intake mods.
In short, buy the exhaust, see how it feels. If it gets really snatchy or starts to run really hot/rough, get it tuned. In most cases, it will be fine. But you wont get the best performance out of the exhaust unless you have it tuned.
BTW, look into the stock 1290 super duke exhaust can...I got mine for $80 plus shipping. Just gotta fashion up a hanger and bam. Its a bit louder than stock, looks better IMO, its lighter than the 1090 exhaust, and its still a stock ktm part! Plus, if you can find it under $100 its def worth it.
Anyways, thats my 0.02