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1. The content of the square brackets, pre-cap, should be around 10 (as an order of magnitude). The cap on the velocity is still 5000 (10000 if you include the possible later multiplication by up to 2).
In order to exceed vel 5000, your modded creature needs a strength of over 50000 (default 1000), OR a weapon speed mod of over 50000 (default 1000), OR some combination of the two. This is unlikely to occur without a deliberate modding attempt.
2. The "/10" is part of an undocumented "volume/10" thing that was tacked on. When the raws say [SIZE:150] for a bolt, the game uses "15" for the volume. My equations equivocate the two volumes, perhaps. Toady's code is also inconsistent on this matter.
3. Armor does not accumulate damage. Any "damage" that it takes (i.e. being penetrated by a bolt) is effectively instantly healed before the next attack, by virtue of the damage numbers being discarded without being saved in any way.
Steel bolt vel 42, momentum 49, contact 5.
Steel armor blunt momentum cost (steel on steel is blunt!) 1781 for contact 252, 35 for contact 5.
49>35 therefore bolt punches a hole in the armor and does edged damage to layers below.
Also since "steel on steel is blunt", a steel mail shirt will convert the attack from an edged attack to a blunt attack without breaking, passing on a momentum 49, contact 5 blunt attack to the layers below. This is because of the flexibility (STRUCTURAL_ELASTICITY_CHAIN_ALL).