Squares for answer choice options and perfect alignment to mathematical answers

The obvious problem is that D is wider than A.

We can get a true square around capital letters by using the height as width:

\documentclass{article}

\newcommand{\squarecap}[1]{\fbox{\makebox[\height]{#1}}}

\begin{document}

\squarecap{A}\par
\squarecap{B}\par
\squarecap{C}\par
\squarecap{D}\par
\squarecap{E}\par
\squarecap{M}\par

\end{document}

The question about the angstrom is of a different kind: \AA=$1$ has no space; if you don't want to use siunitx (which is however recommended), type in

$1\,\textup{\AA} = 10^5\,\textup{fm}$

You can use \eqmakebox[<tag>][<align>]{<stuff>} to have all <stuff> with the same <tag> be set <align>ed in a box of maximum width. Below I've played around with those so you can see what the effect is:

\documentclass{extarticle}

\usepackage[UTF8]{inputenc}

\usepackage{siunitx,eqparbox}

% https://tex.stackexchange.com/a/34412/5764
\makeatletter
\NewDocumentCommand{\eqmathbox}{o O{c} m}{%
  \IfValueTF{#1}
    {\def\eqmathbox@##1##2{\eqmakebox[#1][#2]{$##1##2$}}}
    {\def\eqmathbox@##1##2{\eqmakebox{$##1##2$}}}
  \mathpalette\eqmathbox@{#3}
}
\makeatother

\sisetup{
  per-mode = symbol
}

\newcommand{\makeoption}[2][default]{\fbox{\eqmakebox[#1]{#2}}}
\newcommand{\genericoption}{\rule[-.2\baselineskip]{100pt}{.4pt}}

\begin{document}

\begin{enumerate}
  \item La velocità di \SI{1e2}{\metre\per\second} espressa in \si{\kilo\metre\per\hour} è:

    \makeoption{A} \eqmakebox[first][r]{\SI{36}{km/h}}.     \\
    \makeoption{B} \eqmakebox[first][r]{\SI{360}{km/h}}.    \\
    \makeoption{C} \eqmakebox[first][r]{\SI{27.8}{km/h}}.   \\
    \makeoption{D} \eqmakebox[first][r]{\SI{3.60e8}{km/h}}. \\
    \makeoption{E} \genericoption

  \item In fisica nucleare si usa l'angstrom (simbolo: $\SI{1}{\AA} = \SI{1e-9}{m}$) e il fermi o femtometro ($\SI{1}{fm} = \SI{1e-14}{m}$). 
    Qual è la relazione tra queste due unità di misura?

    \makeoption{A} $\SI{1}{\AA} = \eqmathbox[second][r]{\SI{d5}{fm}}$.   \\
    \makeoption{B} $\SI{1}{\AA} = \eqmathbox[second][r]{\SI{d-5}{fm}}$.  \\
    \makeoption{C} $\SI{1}{\AA} = \eqmathbox[second][r]{\SI{d-15}{fm}}$. \\
    \makeoption{D} $\SI{1}{\AA} = \eqmathbox[second][r]{\SI{d{3}}{fm}}$. \\
    \makeoption{E} \genericoption

\end{enumerate}

\end{document}

I'd suggest using siunitx to set content that has units.

Make the content of all your boxes the same width and don't set your units incorrectly, the spacing and font types are all wrong.

\documentclass{extarticle}

\usepackage{siunitx}

\begin{document}

\fbox{\makebox[0.9em]{A}} $\SI{1}{\angstrom} = \SI{e5}{fm}$.

\fbox{\makebox[0.9em]{B}} $\SI{1}{\angstrom} = \SI{e-5}{fm}$.

\fbox{\makebox[0.9em]{C}} $\SI{1}{\angstrom} = \SI{e-5}{fm}$.

\fbox{\makebox[0.9em]{D}} $\SI{1}{\angstrom} = \SI{e-5}{fm}$.

\fbox{\makebox[0.9em]{E}} \rule{2.2cm}{0.5pt}

\end{document}