Maybe. Maybe not. Depends on the insurance company. Depends on the nature of the modification. Some of them "officially" will not cover any modifications whatsoever, and if in good faith you report that you have made a modification and want it to be covered, the response from the insurance company may be to cancel your policy. Some of them are OK with minor cosmetic things but won't cover "show bikes" (whatever that is!) and most of them won't cover anything that has had "performance modifications" - but sometimes a slip-on muffler is OK, but a Power Commander (even if it's only to fix a driveability problem and not really adding any power!) is not OK. Aftermarket supercharger ... forget it. OEM supercharger ... no problem!
Rightly or wrongly, "don't ask, don't tell" is common. Just don't expect the insurance company to pay for your modifications if there is a claim. It also means that it's probably not a good idea to put a $20,000 paint job and carbon fiber bits on a bike that you are going to be riding every day unless you can afford to take your lumps if something happens.