My early '68 S1 came with the black and silver nose badge. I have read an article from the chap who ordered the first black badges that it had nothing to do with memorializing Jim Clark. But, I also have a Lotus press release from the day stating that the black badges are to memorialize JC's passing.
I've also seen the same article, or at least one similar. The guy who wrote it was Graham Arnold and he was the PR/Sales guy at Lotus in the 60s. In the 70s/80s he also ran Club Lotus, wrote the quarterly newsletter and would fill pages with recollections of "the lighter side of Lotus".
My memory is hazy and I have 2 versions of his tale. The first was that he (GA) had a black S3 FHC put together as his personal / magazine demonstrator car and commissioned some black badges for that. The other is that he'd gone out for quotes and plain black came in cheaper so he bought a batch but Chapman said no until he saw they were cheaper, so they went on the cars.
Having met GA several times in the 70s & 80s at Club Lotus days, my money is on the former because he was that type of guy. In true geek mode I pulled out one of the road tests of that black S3 and I think that clinches it..... Jim Clark died 7th April, 1968. Autosport publication date - 5th April 1968.
Brian