There IS a fundamental flaw in the air filtration system of some Ducati models, including the 1098/1198 series. Well several really - it's a poor design for such an otherwise excellent machine, with poor access etc. - but the problem that allows dust into the airbox relates to an imperfect seal (from stock) where the air intake ducts meet the sides of the airbox. These ducts rely on the dimensions of both the element, which crosses between both ducts, and the airbox itself, to seal from the elements, as well as against the ends of the filter.
Adding a second or thicker gasket at the triangular 'ports' where the ducts meet the sides of the airbox is usually all that is required, and if the element is replaced with the washable K & N filter, such gaskets are supplied with it. The problem is a mismatch of the two dimensions - the width of the filter element, and that of the airbox - as both are meant to seal against the ducts.
But there is no reliability issue with these engines such as you are asking about. I have owned and worked on Ducati twins for 48 years now, and they have just got better and better over this time. Design and quality. I completely dismantled and 'went through' my 1098 engine at 76,000 kms (a long story with pics on this in the forum: I think it was titled Pat's Engine Job or something, if it's still available) and it hardly needed anything. I replaced the piston assemblies, to keep it feeling new, and replaced the big-end shells. And little else, apart from an improved gearchange detent mechanism, and all the fasteners in titanium. Polished rockers, conrods, ports etc etc. It already had Ergal lighweight cam pulleys.
The engine had a remarkable lack of wear, in spite of regular sessions at Phillip Island, and the similarly dusty conditions of rural Australia as those you are concerned about in India (a country I travelled extensively). The 1098 has over 98,000 kms on it now, and still performs as good as new. Modified, lightened, ported, Termignoni exhaust etc etc. A fantastic machine. Apart from the early radiator issues, it has been a trouble-free bike for that distance.
So focus on sealing up your air intake system, and maybe consider a washable K & N filter, with their 'cleaning kit', and continue to enjoy your Ducati. They are a special machine.