It's helpful to consider the case of posets and $\mathbf{2}$-enriched profunctors between them, where $\mathbf{2}$ is the cartesian closed poset $(0 \leq 1)$. (This obviates the complications of coherence conditions when considering what "cocommutative comonoid" should mean.) Maps, i.e., left adjoints in this cartesian bicategory, are simply poset maps in the usual sense -- again, without any attendant complications of having to consider objects up to "Morita equivalence" (cf. semifunctors), since every poset is automatically Cauchy complete in this $\mathbf{2}$-enriched context.
You're quite right that posets maps $f: X \to Y$ are automatically comonoid homomorphisms, but it's worth spelling out some things in detail. First, $f$ considered as a $\mathbf{2}$-profunctor from $X$ to $Y$ is the relation $R: Y \times X \to \mathbf{2}$ where $R(y, x) = 1$ iff $y \leq f(x)$. In general, a relation $R$ is a $\mathbf{2}$-profunctor if
$$R(y, x') \wedge (x' \leq x) \vdash R(y, x), \qquad (y' \leq y) \wedge R(y, x) \vdash R(y', x).$$
The condition that a $\mathbf{2}$-profunctor $R: X \to Y$ is a comonoid homomorphism boils down to the two conditions
$$(\exists y \in Y)\ R(y, x) = 1,$$
$$R(y', x) \wedge R(y'', x) \vdash (\exists y \in Y)\ (y' \leq y) \wedge (y'' \leq y) \wedge R(y, x).$$
Clearly the first condition amounts to a "totality" condition, but the second condition does not imply "well-definedness". For example, if $X$ is a single point $\ast$ and $Y$ is any poset with binary joins, then the maximal relation $R$ where $R(y, \ast) = 1$ for all $y \in Y$ satisfies both conditions.
I don't know any particularly nice characterizations of comonoid maps, even in the simplified setting where we consider just posets. But I will remark that if the "Frobenius conditions" hold in a cartesian bicategory, i.e., if the canonical 2-cells
$$\delta_X \delta_X^\dagger \to (1_X \times \delta_X^\dagger)(\delta_X \times 1_X), \qquad \delta_X \delta_X^\dagger \to (\delta_X^\dagger \times 1_X)(1 \times \delta_X)$$
that are mated to the coassociativity isomorphisms $(1 \times \delta_X)\delta_X \cong (\delta_X \times 1_X)\delta_X$ and its inverse (respectively), are themselves isomorphisms, then it may be shown that every object $X$ is monoidally dual to itself, and that the "opposite" $R^{op}: Y \to X$ of a comonoid homomorphism $R: X \to Y$ is its right adjoint (making $R$ a map) -- much as in the case of Cartesian Bicategories I by Carboni and Walters. This happens for example in the case of groupoids and profunctors between them.