I know the answers to some of these questions, or at least think I do. The disappearance probability is the denominator of the annual probabilty of disappearing. The numerator is always 1. Therefore a value of 200 in this field means that on average the resource will disappear once every 200 years or, more meaningfully, every year there is a 0.5% chance that resource will disappear - and reappear somewhere else as the number is fixed at the start of the game.
The appearance value, I think, is ten times the number of actual tiles, e.g. 160 would correspond to 16 tiles of that resource. I am not sure whether this is a hard value or the centre of a normal distribution, i.e there would be a roughly 90% probability that there would be between 14-18 such tiles, given a std deviation of 1. On a huge map, that is not many tiles. I have bumped huge all the way up to 256x256 which is well over 60,000 tiles. Assume half are water and you need, on average, an empire of 2000 tiles to have one such resource. For this reason I have increased the appearance probability for all resources, to the max of 300 for all the early resources and to a lesser extent for the later resources as empires and capabilities will be greater as the game progresses. It is possible that what I have just explained is only true for an 8 civ game and there is a number of civs dependency in the calculation. Unfortunately, there does not appear to be a map size dependency for this.
You can actually enter values for appearance and disappearance probabilities for luxury resources but I don't know if this has any effects. If anyone knows a way to increase the appearance rate for luxuries, I would love to hear it as it can be pretty frustrating to have 50+ cities and 1 or 2 luxuries, and maybe no 'spares' for trades.
As for the invisible resources past 23, the patch seems to have fixed that. I am playing a modified LWC 0.7 mod (version .8 crashes my computer whenever I discover masonry) with three resources in addition to the cotton and mighty stallions included in the mod. I have just reused some existing icons but they are all visible and they all can be used. Admittedly, all three of my additional resources are bonus resources so I can't say this is also true for luxury and strategic resources.