On the count of compounds there is no limitation directly, however the bulk upload is limited in size of the uploaded file to ~ 100 Mbytes/file.  It can be modified as follows: 

Edit the {tomcat_home}/webapps/RegistryCxn/WEB-INF/classes/applicationContext.xml file and edit the <bean id="multipartResolver">  tag by increasing the value of maxUploadSize  property (after saving the file, you have to restart the server):

<bean id="multipartResolver" class="org.springframework.web.multipart.commons.CommonsMultipartResolver">
<!-- the maximum file size in bytes (100MB) -->
  <property name="maxUploadSize" value="104857600" />