I don't see p1 here

This is a really annoying bug. That's why I putted P1.
The beans.xml could contains specific informations and must be in src/main/webapp, not in the others dierctories.

So, I readed the code, that what I thinks, but as I'm not a netbeans RCP specialist, I let other people check : 

In "Context and Dependency Injection support" (web.beans), we have the WebCdiUtil class.

Line 79 we have this : 
WebModule wm = WebModule.getWebModule(project.getProjectDirectory());

So I understand it could check only one WebModule, the code could be easily modified to give back a WebModule array ?

For exempel, in org.netbeans.modules.web.api.webmodule.WebModule, add : 

    public static List<WebModule> getWebModules (FileObject file) {
        List<WebModule> webModules = new ArrayList<WebModule>();
        Parameters.notNull("file", file); // NOI18N
        Iterator it = implementations.allInstances().iterator();
        while (it.hasNext()) {
            WebModuleProvider impl = (WebModuleProvider)it.next();
            WebModule wm = impl.findWebModule (file);
            if (wm != null) {
                webModules.add(wm);
            }
        }
        return webModules;
    }  

And in org.netbeans.modules.web.beans.WebCdiUtil, change method with

   public Collection<FileObject> getBeansTargetFolder(boolean create) {
        Project project = getProject();
        if (project == null) {
            return Collections.emptyList();
        }
        List<WebModule> wmList = WebModule.getWebModules(project.getProjectDirectory());
        if (wmList != null && wmList.size() > 0) {
            Collection<FileObject> fileObjects = new ArrayList<>();
            for (WebModule wm : wmList) {
                if (wm != null && wm.getDocumentBase() != null) {
                    FileObject webInf = wm.getWebInf();
                    if (webInf == null && create) {
                        try {
                            webInf = FileUtil.createFolder(wm.getDocumentBase(), WEB_INF);
                        } catch (IOException ex) {
                            Logger.getLogger(WebCdiUtil.class.getName()).log(
                                    Level.WARNING, null, ex);
                        }
                    }
                    fileObjects.add(webInf);
                }
            }
            if (fileObjects.size() > 0) {
                return fileObjects;
            }
        }
        return super.getBeansTargetFolder(create);
    }

yes it may be but if look at category cdi, it's some specific use case is broken rather then cdi itself, and no data loss etc.
as it's hard to have a product without issues and the same regarding hints, hints should be configurable i/e/ be able to switch off at least.  
Anyway I like to try to verify next week what you've suggested.

>p2 to be in view for next week

Exactly the same problem with 8.0.2 and filtering in pom.xml:

<plugin>
    <groupId>org.apache.maven.plugins</groupId>
    <artifactId>maven-war-plugin</artifactId>
    <version>2.3</version>
    <configuration>
        <filters>
            <filter>src/main/resources/${myProfile}/filters/ejb-jar.properties</filter>
        </filters>
        <webResources>
            <resource>
                <directory>src/main/webapp/WEB-INF</directory>
                <filtering>true</filtering>
                <targetPath>WEB-INF</targetPath>
                <includes>
                    <include>ejb-jar.xml</include>
                </includes>
            </resource>
        </webResources>
    </configuration>
</plugin>

Ordering problem fixed in web-main a1fe45a117cd.

Fixed in web-main d8081985857b.

Integrated into 'main-silver', will be available in build *201504201004* on http://bits.netbeans.org/dev/nightly/ (upload may still be in progress)

Changeset: http://hg.netbeans.org/main-silver/rev/a1fe45a117cd
User: Petr Hejl <phejl@netbeans.org>
Log: #248687 - Multiple Maven WebResources and beans.xml

tested with 201504290001, and works great!
thanx