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You only have to do this a few hundred times 8-(, once for each thing you want to have away.The same shitty process goes for component reference designators on the F.Sinkscreen and B.Silkscreen layers.
But there is a way to do this in bulk as described here:
Before changing, the reference symbol looks like:
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Step 1. Open ‘Edit’ -> ‘Edit Text & Graphic Properties…’
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Step 2. Select ‘Reference Designators’ on the top left panel; check the filter as ‘F.silkscreen’; Specify the footprint you want to change in ‘Filter items by parent footprint reference’, e.g. ‘R*’, ‘C*’.
Step 3. [The most important one] Uncheck the ‘Visible’ in the ‘Action’ panel.
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Step 4. Done. Here is how it looks after editing:
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