Can we use multi-site with shared server hosting?

This is a bit of a follow on from a couple of previous questions where Ash and Ari gave me some helpful advice that we still need to implement - so thank you both for that. https://premium.wpmudev.org/forums/topic/our-wordpress-was-installed-through-the-bluehost-control-panel-is-that-a-problem and https://premium.wpmudev.org/forums/topic/several-questions-re-performance-with-bluehost-shared-server

Our site seemed to have been throttled by bluehost for 24 hours although it's still in development and has very few users and products. Here's the email I sent them and their response. I have a couple of thoughts which I'll add after this and I'm hoping for some advice because I'm not sure if our whole project needs a rethink.

My email: "We are in the process of developing a website and have tried a few different approaches. We installed wordpress separately, with 3 different themes, on http://www.yourshootshop.com/A , http://www.yourshootshop.com/swap and http://www.yourshootshop.com/W but in the end abandoned those attempts (we probably should have deleted those folders - I'm not sure whether that's relevant) and decided on a multisite installation of wordpress at http://www.yourshootshop.com

We're still at the stage of trying various things to decide on the final structure of our site and have installed but then deactivated or deleted quite a few plugins (which probably hasn't helped) and currently have around 30 active plugins, including marketpress, buddypress and another wordpress classifieds plugin. However we have very few users as we are not yet live.

The site seems to be pretty slow, both for loading pages on the front end and using the back end of wordpress. I had a look at the bluehost cpanel and we appear to have been throttled every hour for the past 24 hours - in spite of the fact that we have not been using it every hour but only now and then as we work on it.

If it's a plugin, either one that is active, or some bits left behind from one that I thought I had deleted or deactivated, then I'm not sure how to identify it.

I'm hoping you could also advise me on something else. We have installed wordpress using the 1-click installation on your cpanel but have been told that this is a bad idea in general, for security reasons, and is particularly discouraged when using buddypress. Should we think about re-installing it manually?"

Their response "I'm sorry to hear of the trouble you're having.
Multisites are nice for flexiblity , but can really slow down sites. If you were running on your own machine it might work.
It really slows the Mysql quires down, because of the back forth on the site.

Please let us know if you have any other questions or concerns. "