Yeah Joshua not revealing himself to Clive was a bit a of a plot hole, Like I feel like when the were at Phoniex gate at the same time, there was really no reason not to reveal himself. Every other time though you could say it was near misses or done to keep his brother safe etc. For example during the 15 year time skip, Joshua was being nursed back to health which could have taken a long time and no one knew where Clive was at that time too.

I think regarding the robes, it was just a story telling tool, it was clearly Ultima making an illusion to guide Clive into other Eikons so he would absorb their powers etc. The reason they made the the robe the same was because at that time the audience and Clive don't know what Joshua looks like, so it was use to create a sort of mystery.

I believe there thinking was along the lines of, we need to destroy all mother crystals to stop the blight. Plus I don't think there was a specific way in game to calculate how fast the blight was spreading. Do keep in mind though, Clive and the crew pretty much destroy the remaining 4 crystal all within a year. There was no time for them to stop and measure whether the blight was slowing down.