The first version does not work, as you suspected. For example, if $Te_n= (1/n)e_{n+1}$ for $n\ge 0$ on $H=\ell^2(\mathbb Z)$, then the $T^n e_0$, $n\ge 0$ are linearly independent. However, we can easily arrange matters in such a way that $T^N(e_0+\delta e_{-1})=0$ for a small $\delta>0$: $T$ will map $e_{-1}$ to $e_{-2}$ and then to $e_{-3}$ etc. We wait until $T^Ne_0$ has the same size as $\delta$, and then we finally map $e_{-N}$ to $-e_N$.
Then we just continue in this way: we define $Te_j$ for $j<-N$ such that $T^{M} (e_0+\delta' e_{-N-1})=0$ for an even smaller $\delta'>0$ etc.
The second claim is true. In fact, the set of vectors $y$ for which $\{T^ny\}$ is l.i. is a dense $G_{\delta}$ set. This follows from the observation that
$$
A_N = \{ y\in H: y,Ty,\ldots , T^N y \:\:\textrm{are l.i.}\}
$$
is a dense open set. It's easy to see that $A_N$ is open, and to prove that it's dense, suppose that we had a $y\in H$ and an $N\ge 1$ such that $y+z\notin A_N$ for all $\|z\|<r$, for some $r>0$. Then, if $N$ was minimal with this property, we have that
$$
T^Nz \in L(y,Ty, \ldots, T^{N-1}y, z, Tz, \ldots T^{N-1} z ) \quad\quad\quad\quad (1)
$$
for all $z$ of small norm. However, since $T$ is linear, (1) then holds for all $z\in H$. Moreover, $T^n z$ for $n\ge N$ lies in the same (at most) $2N$ dimensional space. This contradicts our assumption that there is an $x\in\bigcap A_n$.