Solved after upgrading to v3.1.4
Reference: https://github.com/NodeBB/NodeBB/pull/11533/commits

Thanks @julian for addressing this issue.

I recently deployed my NodeBB in a docker container, and install the plugin locally by copying my plugin into node_modules directory.
When I started the NodeBB server, I got this message:

2023-01-24T08:59:05.922Z [4567/181] - warn: [plugins] "nodebb-plugin-my-plugin" is active but not installed.

This is my Dockerfile content:

FROM node:16.14.0

RUN mkdir -p /usr/src/app &&  chown -R node:node /usr/src/app
WORKDIR /usr/src/app
RUN apt-get install git

ARG NODE_ENV
ENV NODE_ENV $NODE_ENV

COPY --chown=node:node install/package.json /usr/src/app/package.json

USER node

COPY --chown=node:node . /usr/src/app

RUN npm install --only=prod && npm cache clean --force
RUN git clone https://bitbucket.org/dev/nodebb-plugin-my-plugin.git
RUN cp -r nodebb-plugin-my-plugin node_modules/

ENV NODE_ENV=production \
    daemon=false \
    silent=false

EXPOSE 4567

USER root
RUN chown root:root ./ -R

CMD node ./nodebb activate nodebb-plugin-my-plugin; node ./nodebb build; node ./nodebb start -l

The plugin was successfully installed when I run it without docker container.
Please give me some suggestions. Thanks in advance.

@baris thank you! I'll try your solution and update here