TL;DR
- The AGCD problem does require asymptotic exponential time to be solved.
- In general, LLL cannot solve the AGCD problem
- The parameters $(\gamma, \eta, \rho) = (\lambda^5, \lambda^2, \lambda)$ proposed in DGHV10 guarantee (asymptotic) security level of $2^{\Omega(\lambda)}$.
Lattice attacks on the AGCD problem
You are supposing that one can solve the AGCD problem using LLL. Of course, if one can do it, then the AGCD problem is solved in polynomial time. However, this is not true in general, thus, an attacker has to use BKZ with big block size, which is then exponential time.
Roughly speaking, in the AGCD problem, there is a "gap" $\Delta := \eta - \rho$
between the secret value $p$, whose bit length is $\eta$, and the noise terms, whose bit length is $\rho$.
The lattice attacks end up trying to find vectors "in this gap",
that is, vectors that have norm bigger than $2^\rho$ but smaller than $2^\eta$,
thus, we always have necessary conditions of the form
$$ \alpha t + \frac{\gamma}{t} < \eta - \rho ~~~~~ (\text{Inequality }1)$$
where $2^\alpha$ is the root Hermite factor of the lattice-basis reduction algorithm.
For example, in the paper you linked, GGM16, Inequality (4) on page 5, is essentially the same as Inequality (1) above if you
cancel out the term $\sqrt{t+1}$ that appears in both sides and
ignore the constants
$0.47$
and
$\sqrt{1 / (2\pi e)} \approx 0.242$
but don't ignore the exponential approximation factor of LLL.
Intuitively, the smaller this gap is, the harder it is to find a vector "in" this gap.
Typically, when we instantiate the AGCD problem with $\lambda$ bits of security, we set $\rho = \lambda$, so that the attacks on the noise terms take more than $2^\lambda$ steps, and $\eta$ is defined by the application (e.g., it depends on the depth of the circuits to be evaluated homomorphically). Then, we just have to choose $\gamma$ to obtain the desired security level.
And we do this by fixing a root Hermite factor and plugging it in Inequality (1), then solving for $\gamma$.
Ruling out LLL
To choose the parameters such that LLL cannot solve the AGCD problem (which requires then that an attacker uses BKZ, which is an exponential time algorithm), we can set the (optimistic) root Hermite factor of LLL $2^\alpha = 1.02$,
thus, in Inequality (1), we have
$$\log(1.02) t^2 + (\rho - \eta) t + \gamma < 0.$$
But for this Inequality to have a solution, we need its discriminant to be positive, thus, to rule out LLL, we can choose $\gamma$ such that the discriminant is negative, i.e.,
$$(\eta -\rho )^2 - 4 \log(1.02) \gamma < 0
\iff
\gamma > \frac{(\eta -\rho )^2}{ 4 \log(1.02) } \approx 13 \cdot (\eta -\rho )^2. $$
Asymptotic security claimed in DGHV10
Plugging
$(\gamma, \eta, \rho) = (\lambda^5, \lambda^2, \lambda)$
in Inequality (1), we have
$$\alpha t + \lambda^5 / t < \lambda^2 - \lambda \approx \lambda^2,$$
therefore, we must choose
$t \approx \lambda^3$
for the term
$\lambda^5 / t$ to be smaller than the gap $\eta - \rho$,
but then, $\alpha t \approx \lambda^3$ is bigger than the gap.
Hence, we have no solution.