Carbon's role in ocean acidification
In answering this complex question, I think it's important to consider the form of carbon that is utilized and the overall reactions involved (warning: somewhat lengthy diversion ahead, and advance apologies if such is already understood by this audience). In the long-term carbon cycle, atmospheric $\ce{CO_{2,(g)}}$ drives weathering on land, importantly of silicates. $\ce{CO_{2,(g)}}$ dissolves in pure water as aqueous ion ($\ce{CO_{2,(aq)}}$) and carbonic acid ($\ce{H_2CO_{3(aq)}}$).
$$ \ce{CO_{2,(g)} + {H_{2}O_{(l)}}  &lt;=&gt; {H_2CO_{3,(aq)}} }$$
but true carbonic acid is unstable, and the vast majority of this total dissolved carbon is thus present as the aqueous ion $\ce{CO_{2,(aq)}}$, with concentrations obeying the simple Henry's law relation (not shown). We can write this net reaction is
$$ \ce{CO_{2} + {H_{2}O}  &lt;=&gt; {H_2CO_{3,(aq)}} &lt;=&gt; H^{+}_{(aq)} + HCO_^{-}_{3,(aq)} }$$
Bicarbonate also reflects the association/dissociation reaction involving pure carbonate ion,
$$
\ce{H^{+} + CO_^{2-}_{3} &lt;=&gt; HCO_^{-}_{3}}
$$
Weathering of a continental silicate, e.g., a normative wollastonite (chosen for simplicity), can thus be written as$$
\ce{ CaSiO_3 + H_{2}O +2CO_{2} -&gt; 2 HCO_^{-}_{3} + Ca^{2+} + SiO_{2}}
$$
The important point is that the dissolved carbon delivered to seawater by continental weathering is as bicarbonate, and surface seawater pH ($\sim 8)$ in approximate equilibrium with atmospheric $\ce{CO_{2}}$ indeed reflects this distribution of dissolved species. If we write the equilibrium for skeletal calcium carbonate as
$$\ce{ CaCO_{3} &lt;=&gt; CO_^{2-}_{3} + Ca^{2+}}$$
we can combine the above equations to give the overall reaction for the dissolution/precipitation of $\ce{CaCO_3}$ in seawater (incorporating the mass balance on $\ce{CO_2}$ from reactions 1, 2, 3, and 5 -- sorry I can't get MathJax to turn equation numbering on) as,
$$
\ce{CaCO_{3} + H_{2}O + CO_{2} = Ca^{2+} + 2HCO_^{-}_{3} }
$$
Thus in this context, an important result is that, in the overall mass balance associated with precipitation of $\ce{CaCO_{3}}$ (i.e., driving the above reaction to the left), $\ce{CaCO_{3}}$ serves as a source, not a sink of carbon, because it liberates one mole of $\ce{CO_2}$ originally delivered as bicarbonate to seawater from silicate weathering. In the larger view (long term geochemical cycling), marine carbonates are a temporary sink for carbon that is ultimately subducted and returned to the atmosphere by vulcanism and other magmatic processes. The carbonates residing on the continents today (e.g., Paleozoic) have, in contrast, a much longer residence or cycling time that their modern pelagic equivalents.

Now, to your question: ocean acidification (titration of seawater by atmospheric $\ce{CO_2}$, driving the last reaction to the right) per se is buffered by the attack of this sink of $\ce{CaCO_3}$ producing more bicarbonate. Sequestration of carbon by growing shellfish will, according to the above, consume (some of) this bicarbonate, and produce $\ce{CO_2}$ as a result. The larger, key question to me, is the rate at which the existing store of sedimentary $\ce{CaCO_3}$, particularly in surface water where it is being formed, dissolves in response to this attack.

Edited for clarity, typos