The web application we develop uses three Java Applets.
We know that Chrome 45 will drop NPAPI support. In this page, Oracle says that Java Plugin relies on NPAPI.>
1) Most likely either you re-enabled NPAPI support yourself, or you are in a managed environment that re-enabled NPAPI support for you. You can check chrome://flags to see if it's enabled.
2) No, your applets won't work in Chrome once NPAPI support is completely removed (that's why the infobar you describe is there).