When a beacon beam transitions through water (cobweb, leaves), subsequent recoloration transitions of the beam is delayed. See attached small screencast for evidence.
The position of water along the beam, or the position of stained glass relative to the water: these do not matter.
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Confirmed.
Confirmed in 1.8.3.

Is this still an issue in the most recent versions (currently that is 1.10.2, or 16w42a) of Minecraft? If so, please update the affected versions and help us keeping this ticket updated from time to time.

Can confirm in 1.13-pre3.
Beacon updates have become slow in the snapshots for 1.13 (see MC-121105), but cobwebs and water continue to slow it down more.
Confirmed for 1.13.1.