Thanks for all the good vibes, everyone! I'm glad y'all find the site useful.
They show up in the default view, whether they show up after filtering/sorting is dependent on how you filter/sort. One thing to be aware of is that if you sort by a column other than name, if there's no data available for that weapon in that column, it will hide it from the list. So for example, if you sort by DPP, if I'm not able to calculate the DPP for a weapon due to missing data, I don't show that weapon in the list -- I put this in the question-mark popup next to the hidden items list, but it may not be that obvious. The assumption is that if you are sorting by DPP, for example, then you probably aren't interesting in seeing weapons for which this can't be obtained. In the case of your swords, the 45 and 55 are missing a bunch of data, so they are not going to show up for anything other than a name-sorted list. The 35 and 40 do show up for me in other views, so maybe you had filtered them out somehow.
I don't think I ever noticed the show/hide columns feature on EP; but yes, it's not a bad idea.
As a side note to the over-amp problem, one feature I thought might be cool is an option to "pick the best amp", and have it automatically select the amp most appropriate for each weapon and show that in the list. This way you could just put in your professional levels and essentially see the best setups for you.
BTW, I am working on a replacement for the compare tool as we speak.