This integral is not equal to zero.
We may obtain the following closed form.
$$
\begin{align}
\int_0^1 \left(\left\{\frac{1}{x}\right\}-\frac{1}{2}\right)\frac{\log(x)}{x}
\mathrm{d}x & = \dfrac{\ln^2(2\pi)}{4}-\dfrac{\gamma^2}{4}+\dfrac{\pi^2}{48}-\dfrac{\gamma_1}{2}-1\tag1 \\\\
\end{align}
$$
where $\left\{x\right\}$ denotes the fractional part of $x$, $\gamma$ denotes the Euler–Mascheroni constant and where $\gamma_{1}$ denotes the Stieltjes constant defined by
$$
\gamma_{1} = \lim_{N \rightarrow \infty}\left(\sum_{k=1}^{N}\frac{\ln k}{k}-\frac{\ln^{2}N}{2} \right).
$$
Consequently, we have the numerical evaluation:
$$
\begin{align}
\int_0^1 \left(\left\{\frac{1}{x}\right\}-\frac{1}{2}\right)\frac{\log(x)}{x}
\mathrm{d}x = \color{red}{0.00}31782279542924256050500... . \tag2
\end{align}
$$
Here is an approach.
Step 1. Let $s$ be a complex number such that $0<\Re{s}<1$. Then
$$
\int_{0}^{1} x^{s-1}\left\{\frac{1}{x}\right\}\mathrm{d}x = -\frac{1}{1-s} -\frac{\zeta(s)}{s}\tag3
$$ where $\left\{x\right\}$ denotes the fractional part of $x$ and where $\zeta$ denotes the Riemann zeta function.
Proof. Let us assume that $0<\Re{s}<1$. We may write
$$
\begin{align}
\int_{0}^{1} x^{s-1}\left\{\frac{1}{x}\right\}\mathrm{d}x & = \sum_{k=1}^{\infty}
\int_{1/(k+1)}^{1/k} x^{s-1}\left\{\frac{1}{x}\right\}\mathrm{d}x \\
& = \sum_{k=1}^{\infty} \int_{k}^{k+1} \left\{x\right\} \frac{\mathrm{d}x}{x^{s+1}} \\
& = \sum_{k=1}^{\infty} \int_{k}^{k+1} (x-k) \frac{\mathrm{d}x}{x^{s+1}} \\
& = \sum_{k=1}^{\infty} \int_{0}^{1}\frac{v}{(v+k)^{s+1}}\mathrm{d}v \\
& = \sum_{k=1}^{\infty} \int_{0}^{1}\left(\frac{1}{(v+k)^{s}}-\frac{k}{(v+k)^{s+1}}\right)\mathrm{d}v \\
& = \sum_{k=1}^{\infty} \left.\left(\frac{1}{(-s+1)(v+k)^{s-1}} +\frac{k}{s(v+k)^s}\right) \right|_{0}^{1} \\
& = -\frac{1}{1-s}-\frac{\zeta(s)}{s}.
\end{align}
$$
Step 2. We have
$$
\int_{0}^{1} x^{s-1}\left(\left\{\frac{1}{x}\right\}-\frac{1}{2}\right)\log(x)\mathrm{d}x = -\frac{1}{(1-s)^2} +\frac{1}{2s^2} +\frac{\zeta(s)}{s^2} -\frac{\zeta'(s)}{s}. \tag4
$$
Using $(3)$, we readily get
$$
\int_{0}^{1} x^{s-1}\left(\left\{\frac{1}{x}\right\}-\frac{1}{2}\right)\mathrm{d}x = -\frac{1}{1-s}-\frac{1}{2s} -\frac{\zeta(s)}{s}
$$
which we differentiate with respect to $s$ to obtain $(4)$.
Step 3. For $s$ near $0$, we take into account the Taylor series expansion of the Riemann $\zeta$ function:
$$
\begin{align}
& \zeta(s) =-\frac12-\dfrac{\ln(2\pi)}{2} s +\left(\dfrac{\gamma^2}{4}-\dfrac{\pi^2}{48}+\ln(2\pi)-\dfrac{\ln^2(2\pi)}{4}+\dfrac{\gamma_1}{2}\right)s^2+\mathcal{O}(s^3)
\\& \zeta'(s) =-\dfrac{\ln(2\pi)}{2} +\left(\dfrac{\gamma^2}{2}-\dfrac{\pi^2}{24}+2\ln(2\pi)-\dfrac{\ln^2(2\pi)}{2}+\gamma_1\right)s+\mathcal{O}(s^2)
\end{align}
$$
and upon letting $s$ tend to $0^+$ in $(4)$ we obtain $(1)$.
Remark: A related result to $(3)$.
Best Answer
Enforce the substitution $x\mapsto\frac 1x$ in your latter integral to obtain $$\small\int_1^\infty\log\left|\frac{1+x}{1-x}\right|\frac{{\rm d}x}x\stackrel{x\mapsto\frac 1x}=-\int_1^0\log\left|\frac{1+\frac1x}{1-\frac1x}\right|\frac1{\frac1x}\frac{{\rm d}x}{x^2}=\int_0^1\log\left|\frac{x+1}{x-1}\right|\frac{{\rm d}x}x=\int_0^1\log\left|\frac{1+x}{1-x}\right|\frac{{\rm d}x}x$$
Continuing by letting $x\mapsto\frac{1-x}{1+x}$ gives $$\int_0^1\log\left|\frac{1+x}{1-x}\right|\frac{{\rm d}x}x\stackrel{x\mapsto\frac{1-x}{1+x}}=-\int_0^1\log\left|\frac1x\right|\frac{2\,{\rm d}x}{1-x^2}=-2\int_0^1\frac{\log x}{1-x^2}\,{\rm d}x$$ Using the geometric series yields $$-2\int_0^1\frac{\log x}{1-x^2}\,{\rm d}x=-2\sum_{n\ge0}\int_0^1 x^{2n}\log x\,{\rm d}x=2\sum_{n\ge0}\frac1{(2n+1)^2}$$ Finally, since $\sum_{n\ge0}\frac1{(2n+1)^2}=\frac34\sum_{n\ge1}\frac1{n^2}=\frac34\zeta(2)$, we obtain