You probably could do the bulk convert on a Mac running numbers. You may have to write a script to automate.
You could try another spreadsheet app and see if it could work with .xls without conversion. You may consider another backup site like dropbox.com so that you have two/three copies of your files.
All of the "Office" document editing applications on the iPad have limitations. Best try them out to see if they meet your needs.
Free apps
iWork by Apple -- free with newly purchased iPads
http://www.imore.com/how-get-all-iwork-apps-iphoto-and-imovie-free-eligible-ipho ne-or-ipad
iWork for iCloud Beta
https://www.apple.com/iwork-for-icloud/
Quickoffice
Quickoffice is an application available for iOS and Android tablets and phones that lets you view, create, and edit Microsoft Office, as well as view and annotate PDF files. Connect Google Drive to Quickoffice for cloud storage so that you can easily access and edit files from your tablet, phone, or computer and know that your files are always up-to-date
https://support.google.com/quickoffice/answer/2986862?hl=en&ref_topic=2986859
Kingsoft Office
"Read, edit PowerPoint files, and read Word documents on your iPhone or iPad, Share it by cloud storage."
http://www.kingsoftstore.com/office-free-ios
CloudOn
Client front end to a Microsoft Office running on a server
"CloudOn brings Microsoft Office® to your iPhone & iPad and links it to your Box, Dropbox, Google Drive and SkyDrive accounts." Free for a give number of documents.
https://itunes.apple.com/us/app/cloudon/id474025452?mt=8
Microsoft read only apps for Excel, Powerpoint and Word
https://itunes.apple.com/us/app/microsoft-excel-for-ipad/id586683407?mt=8
https://itunes.apple.com/us/app/microsoft-powerpoint-for-ipad/id586449534?mt=8
https://itunes.apple.com/us/app/microsoft-word-for-ipad/id586447913?mt=8
Paid
DocsToGo
• VIEW/EDIT/CREATE Word & Excel files(Office 2007/2008/2010)
• VIEW PowerPoint, PDF, iWork, Text, .RTF, and more!
• Send & receive attached supported documents using the built-in Mail app
• FREE desktop application with your purchase! Compatible on Win & Mac allows you 2-way file sync with a WIFI connection.
• Open & Edit files within DocsToGo from any 3rd party app that supports the “Open In” feature
• Supports iTunes File Sharing via USB cable for manually moving files
https://itunes.apple.com/us/app/documents-to-go-office-suite/id317117961?mt=8
Thanks to Texas Mac Man for pointing to this link.
"Quickoffice Connect Mobile Suite and Documents To Go These two apps share an important feature: unlike Numbers, they can open, edit, and save an Excel spreadsheet without stripping out any data or formatting, even though they can’t display or edit all the existing information; spreadsheets can make the round trip from Mac to iPad and back safely, without losing anything."
http://www.macworld.com/article/1159958/ipadspreadsheet.html
Office² HD
"Office² HD, the most intuitive and straightforward office document editor available on the iPad, makes it easy to open, view, create and edit Word (DOC & DOCX), Excel (XLS & XLSX), and PowerPoint (PPT & PPTX) files right from your iPad!"
https://itunes.apple.com/us/app/office2-hd/id364361728?mt=8
Office 365
Office Mobile for iPhone requires a qualifying Office 365 subscription
* Edit - You can make quick edits to Word, Excel and PowerPoint documents.
* Documents Remain Intact - Formatting and content remain intact when you edit Word, Excel, or PowerPoint documents on your phone.
* Edit While Offline - Your device doesn’t have to be continuously connected to the network to work on an Office document that is stored online. You can view and edit recently used documents even while you’re offline. Your changes will be saved online when your device reconnects to the network or to Wi-Fi.
* Create – You can create new Word and Excel documents on your phone.
https://itunes.apple.com/en/app/office-mobile-for-office-365/id541164041?mt=8
