Technically, there is no real warranty from Ruger, but they will repair your defective gun at no charge even if you have modified it. That of course is if the problem is NOT due to the modification but due to a manufacturers defect. They will however remove any modified parts and replace them with factory parts at your expense. I would suggest that if you do any modifications, make sure you keep a replacement part or the original parts just in case you should ever need to return the gun to Ruger.
By the way, does the LCI get in the way of your sights, or do you just not like the look of it when it is raised? My SR9c has the same LCI but it is completely invisible when sighting a target, but is is very visible (as it was meant to be) when just looking at it.