It really depends. The
Disneyland Hotel is truly amazing. The theming, the CMs, the ease of access to the DtD area and the parks. It's magical. But, you'll have just as magical of a time staying on Harbor. I've never personally stayed at HoJo (shockingly! We've pretty much stayed at almost every hotel/motel up and down Harbor at least once). The security lines used to be a real problem a few years ago, but they've since increased the amount of "lanes" that are open in the morning so there is very rarely a huge line or even much of a line at all.
There are a few unhoused/homeless people that tend to hang around Harbor, but they leave you alone and are not really a major threat. There are always people from the parks walking back up to an hour after park closing, so there is very much a safety in numbers aspect there as well. I like to check CrimeMapping for the area around Disneyland and there is very rarely any kind of violent incident in the area, including on Harbor.
We were always Harbor/across the street people growing up and have always had a great time. We had the privilege of staying at the Disneyland Hotel for the first time last year in March and then two more times on-property since then (GCH x1, DLH x2). We are booked for the Disneyland Hotel for Christmas/New Year's again this year, but for our trip coming up in April we are going to do across the street at the Desert Inn. If the $1000 extra feels like it might stretch things too much or make it so you'll not be able to get the souvenirs or meals you want, go with HoJo. You really can't go wrong with either choice.
Also - I don't know if I buy in to the "bubble", at least for Disneyland. Walking through DtD can be interesting with a lot of things to look at, but the experience isn't diminished by going across the street to off-property. I almost miss walking under the big "Disneyland Resort" sign every morning when we're on-site. Something about it just makes you think...we're actually here!
