Equation environment, equation number parenthesis, are both righthanded

I was able to successfully compile the thesis.tex file included in the distribution after some changes which I will list later.

Regarding your question, I found that all the parentheses in the numbers of the equations were fine.

Just in case I have included samples of the sample paper for the amsmath package. Filename: testmath.tex to check other delimiters. No problems found.

Changes

(1) Font. I did not have the font David CLM, but I found the DavidCLM font already in my system directory. (Perhaps from David Libre from a former project. See What Hebrew fonts can I substitute for David in LuaLaTeX or XeLaTeX?)

So I commented line 133 of iitthesis.cls and defined a newfontfamily in the preamble pointing to the right place.

(2) In the file my-thesis-specific.tex I changed renewcommandlips@dolipsum{ for newcommandlips@dolipsum{ to eliminate the ! LaTeX Error: Command lips@dolipsum undefined.

Note The full kit obtained from the official site https://github.com/eyalroz/technion-iit-thesis/ instead of Overleaf does not have this problem. (fixed on Mar 7, 2020)

(3) I removed an error message (coming from the paragraph before the last in abstractHebrew{) commenting include{front/abstract}. Other Hebrew text were typeset OK. See last figure

Eq. 3.1

This is the new thesis.tex

documentclass[PhD,noabbrevs]{misc/iitthesis}

include{misc/thesis-fields}
include{front/personal-acks}
 %include{front/abstract}
include{front/abbrevs}

usepackage{misc/iitthesis-extra}

include{misc/my-general}
include{misc/my-thesis-specific}

usepackage{multibib}
newcites{pubinfo}{Acknowledgement page references}
defiitthesisextramultibibdefs{}
        
usepackage{amsmath} % added to test eq. samples <<<<<<<<<<<<<<<<<<<<<<<<<<<<

    %newfontfamilyhebrewfont[Script=Hebrew]{David CLM} % changed: line 133 of iitthesis.cls <<<<<<<<<<<
    newfontfamilyhebrewfont[% added <<<<<<<<<<<<<<<<<<<<<
    Path =C:/Windows/Fonts/,%
    Script=Hebrew,%
    Language = Hebrew ,
    Extension =.ttf,%
    UprightFont =*-Medium,%
    BoldFont =*-Bold,%
    ItalicFont =*-MediumItalic,%
    BoldItalicFont =*-BoldItalic%
    ]{DavidCLM} 

begin{document}
    

makefrontmatter
include{main/intro} 
include{main/prelims}
include{main/mainchap1}

include{main/short_testmath} % added <<<<<<<<<<<<<<<

include{main/conclusion}
appendix
include{main/appendix1}
makebackmatter 
end{document}

This is the file short_testmath.tex

%% file short_testmath.tex

newcommand{wt}{widetilde}
newcommand{wh}{widehat}

section{Introduction}

This paper contains examples of various features from AmS-LaTeX{}.

Sample Paper for the textbf{amsmath} Package.

 File name: textbf{testmath.tex}

section{Enumeration of Hamiltonian paths in a graph}

Let $mathbf{A}=(a_{ij})$ be the adjacency matrix of graph $G$. The
corresponding Kirchhoff matrix $mathbf{K}=(k_{ij})$ is obtained from
$mathbf{A}$ by replacing in $-mathbf{A}$ each diagonal entry by the
degree of its corresponding vertex; i.e., the $i$th diagonal entry is
identified with the degree of the $i$th vertex. It is well known that
begin{equation}
detmathbf{K}(i|i)=text{ the number of spanning trees of $G$},
quad i=1,dots,n
end{equation}


Let $C_{i(j)}$ be the set of graphs obtained from $G$ by attaching edge
$(v_iv_j)$ to each spanning tree of $G$. Denote by $C_i=bigcup_j
C_{i(j)}$. It is obvious that the collection of Hamiltonian cycles is a
subset of $C_i$. Note that the cardinality of $C_i$ is $k_{ii}det
mathbf{K}(i|i)$. Let $wh X={hat x_1,dots,hat x_n}$.


begin{equation}label{H-cycles}
biggl(prod^n_{,j=1}hat x_jbiggr)H_c=frac{1}{2}hat k_{ij}det
wh{mathbf{K}}(i|i),qquad i=1,dots,n.
end{equation}

Then, it follows that
%begin{lem}label{lem-det}
begin{equation}label{detprod}
prod_{iinmathbf{n}}
biggl(sum_{,jinmathbf{n}}b_{ij}hat y_jbiggr)
=biggl(prod_{,iinmathbf{n}}hat y_ibiggr)detmathbf{B}.
end{equation}


begin{equation}label{detB}
detmathbf{B}=
sum^n_{l =0}sum_{I_l subseteq n}
prod_{iin I_l}(b_{ii}-lambda_i)
detmathbf{B}^{(lambda)}(I_l |I_l ),
end{equation}


begin{equation}
mathbf{K}(t,t_1,dots,t_n)
=begin{pmatrix} D_1t&-a_{12}t_2&dots&-a_{1n}t_n
-a_{21}t_1&D_2t&dots&-a_{2n}t_n
hdotsfor[2]{4}
-a_{n1}t_1&-a_{n2}t_2&dots&D_ntend{pmatrix},
end{equation}

begin{equation}label{j:mark}
begin{split}
H_c=&
frac{n_1!,n_2!,n_3!}
{n_1+n_2+n_3}sum_ileft[binom{n_1}{i}
binom{n_2}{n_3-n_1+i}binom{n_3}{n_3-n_2+i}right.
&+left.binom{n_1-1}{i}
binom{n_2-1}{n_3-n_1+i}
binom{n_3-1}{n_3-n_2+i}right].end{split}
end{equation}