confused about resource system

The planet's percentages for a resource are a modifier for how much resources that planet will produce. So if your mineral miners are producing 1000 minerals, a planet with 150% minerals will increase that to 1500 minerals. So yes, it does help to build resource extractors on planets with higher percentages.

the 70,000 you're seeing is probably your resource storage. Your facilities produce resources each turn, these resources if not used are stored up to a certain amount the rest are "wasted" You can check how much your empire is storing and producing at the treasury screen (dunno if thats the correct name, but it looks like a crown) Storage facilities will increase your overall storage

That happens when your construction costs shift. Mineral deficits are very common when you retrofit entire structures in your empire as every single planet in your empire suddenly begins burning maximum minerals per turn upgrading all the stuff which is often built purely with minerals. It is arguably the case that in the default game, minerals are the only resource that tends to matter since the demand for them outstrips any other resource, even if you're an organic/crystalline race. Build lots of mineral stores to buffer you against these shortages, and get resource converters to dump your surplus of other-things into minerals. I tend to do this because most of my mineral harvesting comes from Monolith tools or Crystalsolars, which produce all 3 resources in equal base amounts, so I always tend to have whackloads of everything else.

In addition to what Fishman said, you can check where exactly your resources are going on the treasury screen (Resource expenditure). They're either going to maintenance or construction, and you can tell exactly what is costing so much in the construction queue or maintenance by checking ship maintenance costs (ship lists) and facility maintenance costs (colony lists)
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