Since the matrix $D$ doesn't need to be orthogonal, the vector doesn't need to be rotated only. And since $u$ doesn't need to be an eigenvector of $D$, the vector doesn't need to be scaled only. And translation, well you cannot translate a vector, anyway. So in this sense, the vector can indeed change completely if nothing else than double-centredness is known about $D$.
But you're right in that $D\mathbf{u}$ should be centred (in case with a centred vector you mean one whose element sum is $0$). This can be seen quite easily (using $\mathbf{d}_i$ to denote the $i$th row of $D$):
$\mathbf{v} = D\mathbf{u} = (\langle\mathbf{d}_i,\mathbf{u}\rangle)_{i=1}^n$
$\sum_{i=1}^n{v_i}=\sum_{i=1}^n{\langle\mathbf{d}_i,\mathbf{u}\rangle} = \left\langle\sum_{i=1}^n{\mathbf{d}_i},\mathbf{u}\right\rangle=\langle\mathbf{0},\mathbf{u}\rangle=0$
So in fact only $D$'s columns need to be centred in order to make $D\mathbf{u}$ centred.
The answer is yes, since the exponential map $\exp: \mathbf{so}(3) \rightarrow \mathbf{SO}(3)$ is surjective (=onto).
Long answer:
Axis-angle can be represented using a $3$-vector $\omega$ while the magnitude $\theta=|\omega|$ is the rotation angle and $\mathbf{u}=^\omega/_\theta$ is the rotation axis. 3-Vectors are closed under the cross product:
$$\omega_1\in \mathbb{R}^3, \omega_2\in \mathbb{R}^3\Rightarrow (\omega_1\times \omega_2)\in\mathbb{R}^3.$$
Each such vector $\omega$ has an equivalent $3\times 3$ matrix representation
$\hat{\omega}$ (which is uniquely defined by $\hat{\omega}\cdot \mathbf{a} := \omega\times \mathbf{a}$ for $\mathbf{a}$ being a general 3-vector).
The space of matrices of the form $\hat{\omega}$ is called the Lie algebra $\mathbf{so}(3)$. Thus, one can show that matrices of the form $\hat{\omega}$ are closed under the Lie bracket $[A,B]=AB-BA$:
$$\hat{\omega_1}\in \mathbf{so}(3), \hat{\omega_2}\in \mathbf{so}(3)\Rightarrow [\hat{\omega}_1, \hat{\omega}_2]\in\mathbf{so}(3).$$
Now, let us consider the matrix exponential: $\exp(\mathtt{A}) = \sum_{i=0}^\infty \frac{\mathtt{A}^i}{i!} $. Two poperties can be shown:
(1) If $\hat{\omega}\in\mathbf{so}(3)$, then $\exp(\hat{\omega})\in\mathbf{SO}(3)$.
$\mathbf{SO}(3)$ is the special orthogonal group in three dimensions. Thus, it consists of matrices which are orthogonal ($\mathtt{R}\cdot \mathtt{R}^\top=\mathtt{I}$) and the determinant is 1. In other word, it is the group of pure rotations.
(2) The exponential map $\exp: \mathbf{so}(3) \rightarrow \mathbf{SO}(3)$ is surjective.
So, (1) says that every $\exp(\hat{\omega})$ is a rotation matrix. And, (2) says that for each rotation matrix $\mathtt{R}$, there is at least one axis-angle
representation $\omega$ so that $\exp(\hat{\omega})=\mathtt{R}$
Proofs of (1) and (2) are in corresponding text books, e.g. [Gallier, page 24].
Best Answer
If you think about multiplying by a matrix on the left as applying a transformation, then the transformation $B(A(v))$ would be represented in multiplication notation as $BAv$. $v$ gets multiplied by $A$ first and then $B$, which is what you want. By associativity of multiplication, you could also multiply $BA$ first and then multiply this matrix with $v$.