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Coffee is an anti-thiamine factor (because of compounds like caffeic acid, which also exist in Dcaf). It also hinders absorption of thiamine and minerals such as iron. Other than modifying nutrient absorption, it also has benefits, such as raising stomach acid, which is beneficial for protein rich meals. So coffee with a real breakfast (eg., hash browns and eggs) should be beneficial.

Coffee on an empty stomach is not good over repeated long term occasions, as it leads to cortisol spikes. If empty-stomaching coffee, it is a good time to pop some trace metal and mineral pills (iron, manganese, zinc, selenium, chromium, moly, boron, magnesium).

Any problems with thiamine are easily reversed via thiamine supplementation. I try to take B-50 complex two or three times a week, and a thiamine supplement on alternate days, roughly at the same frequency.

Coffee does seem to have net benefits. It's good against brain cloud.