One way you could achieve this is by using a resource filters extension. The resource filters extension allows plug-ins to define filters that are useful for filtering out file types in the resource navigator view.
<?xml version="1.0" encoding="UTF-8"?>
<?eclipse version="3.4"?>
<plugin>
<extension point="org.eclipse.ui.navigator.navigatorContent">
<commonFilter
description="Hides node_modules folder"
id="com.pilot.plugins.nodefilter"
name="node_modules"
activeByDefault="true">
<filterExpression>
<and>
<adapt type="org.eclipse.core.resources.IResource">
<test property="org.eclipse.core.resources.name" value="node_modules"/>
</adapt>
</and>
</filterExpression>
</commonFilter>
</extension>
<extension point="org.eclipse.ui.navigator.viewer">
<viewerContentBinding
viewerId="org.eclipse.ui.navigator.ProjectExplorer">
<includes>
<contentExtension pattern="com.pilot.plugins.nodefilter"/>
</includes>
</viewerContentBinding>
</extension>