What do the different columns in the results show?

Recipe: Name of the recipe
Machines: Number of crafting machines set to the recipe
% Up: Number of crafts actually completed divided by the maximum number of crafts if all machines set to this recipe were working at full capacity
Amount: Amount of ingredient consumed by the recipe being completed once
Crafts: Number of times the recipe has been completed
Total: Total amount of ingredient consumed by this recipe
Per min: Total amount of ingredient consumed by the recipe per minute
%: Percentage of all consumption attributed to this recipe

Why does the item/fluid selector also show irrelevant virtual signals?

This is unfortunately a modding API limitation—it's essentially impossible to allow selection of both items and fluids using a single button without also showing virtual signals. Mods like Factory Planner that do it appear to re-implement that selection UI from scratch.

How frequently does the mod poll the monitored entities?

While a run is active, the relevant entities are checked on once every 60 ticks (once every second).

What if an entity completes a recipe multiple times during that second? Won't those completions be missed?

No. Its consumption will still be accurately counted. The polling rate only actually impacts how frequently the results are getting updated in the mod GUI.

Why is the mod called Production Analyst when it's actually monitoring consumption?

Because it's a catchier name. I'm also considering making it look at item/fluid production as well. That's not very useful in vanilla, but it can be useful in modded games with common byproducts.