Well - not saying that you don't need it. But usually you can make use of wildcards, recursing, whitelists/blacklists etc to make the number actual inputs.conf stanzas more manageable. Perhaps that is not possible in your case.
It sounds like that could be simplified somehow. I've never heard of anything like a 1000 stanzas in a single inputs.conf. To me, 50 would be a rather large inputs.conf.
What's your scenario?