Booking accommodations in smaller cities

What do the "Terms & Conditions" blurb on whatever site you are looking at say?

Hard to address your question(s) without some specifics

Checking for a random week in Verona in November there are 1006 total listings and 65 hotel listings . The largest set of listings is for apartments, but that leaves over 300 non-apartment listings. That seems to be a reasonable set of choices. As usual, planning ahead and doing your own research will remain very important.

We book apartments through Bookings frequently in small towns. Most just expect you to keep it as clean as when you arrive, but no floor washing or laundry. What is important, though, is to note if there is a cleaning fee which sometimes is easy to miss and can be high (not all have them). If you want a hotel, you can indicate on the sidebar for the search. In cities where vacation rentals price out locals, like Lisbon or Venice, we usually use hotels.

There a hotels in both Verona and Bologna so you don't have to have an apartment. I travel to run races in Italy and frequently prefer to have an apartment and even in some of the march smaller towns there have been small hotels to stay in (hiking the Via Francigena I chose both small hotels and B&Bs). Some places on booking.com have begun adding cleaning fees.... you can see it listed. I haven't left anything spotless.

There are mamy hotels in both places

I wonder if you had the filter set to search for “apartments “ inadvertently?

thanks. Definitely didn't apply any filters. A few hotels did come through but most of the listings were B&Bs or apartments. I was only worried about hidden costs and that they weren't legitimate (in that they weren't allowed in some other cities).

What are your dates?
How many nights?

Italy does have pretty strict waste disposal regulations, so if you are not interested in sorting the recycling, it's best to stick to hotels. I have noticed it becoming more cumbersome the last few years, but I have always found owners willing to be flexible and forgiving if I don't get it completely right. (It is not one bin--it is several, and they are picked up on different days of the week.)
I have never noticed anything unreasonable about cleaning. Fees are stated on the booking.
Those places have plenty of hotels, so I am thinking either your search parameters or the dates are affecting your search results.

The apartment listings are probably mostly singles--one listing = one apartment. Hotels often have a dozen or more rooms; large hotels may have over 100 rooms. Therefore, the number of listings in each category isn't indicative of the number of rooms in each category.