Hello!

The photos for both the apple tree and shrubs are not good enough to be able to tell what is afflicting them. Neither is the photo of the leafed out shrub good enough to tell what kind of shrub it is.

The presence of a culprit doesn't mean it's the only answer for all the issues affecting the apple tree. I see that the rock mulch may be hiding the tree's root flare and if that's been the case for a long enough time, the roots may be encircling the trunk.  I recommend digging down into the rock mulch to find the root flare and check for stem girdling.  Here is more information about stem girdling.

Stem girdling can cause stress in a tree that can be seen in fewer leaves, less fruit production, and opportunistic insect and disease attacks such as fire blight.

The best I can tell from the photos is that the bumps on both the tree and shrubs may be scale, an insect. The presence of scale may make sense on the shrub but I'm not familiar with scale showing up on trees after the bark has been removed.

Do you recall any flowers on the shrubs? When did they bloom, what color, and their form? This may help me figure it out. It may require waiting until they leaf out again this spring in order to get some really good close-up photos. Feel free to submit a new question with those when that happens.

In the meantime, you could send a symptomatic twig or branch from the shrub to the U of MN Extension Plant Disease Clinic for a diagnosis. They may be able to figure out what the shrub is and what the issue is. Here is their link where you'll learn about their services, prices, and how to submit a sample.

As for the tree, I recommend enlisting the help of a certified arborist who can evaluate the tree for all issues. Here is a link to information about how to find and hire a professional.

Best of luck!