Can't answer the first question but can have a stab at the second. A hash calculation can be quite time consuming since it has to examine the file and generate a unique number that will ensure that a modified file will not be recognised as the original. Since it appears you have extracted all of the .net framework into its individual files, there are lot of files to check whereas if you simply distributed the original .exe there would only be one file to check. I've always found it better to use the packed original since there is little real benefit in extracting the files first and it will often make the whole distribution process much slower.
Mark Star - http://www.marxtar.com
Home of Power State Notifier & Wake-On-WAN for LANDesk
It only needs to calculate the hashes the first time you push out a package. It has to read the entire contents of each file, and create a hash for it. On small files like .net 1.1, it should take more than a couple minutes. Go into the console, right click on the package, and choose reset package hash. That will force it to re calculate. More than an hour is very unusual. I would delete the files, and re-copy them.
I've just upgraded to 8.8 SP1 and experiencing the same problem, taking a very long time to Hash files!!!
Do you find a solution to your problem?